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Rebuild perl-test-pod-coverage #12654

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merged 2 commits into from
Dec 14, 2018
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@druvus druvus commented Dec 14, 2018

  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

@druvus druvus merged commit 4f3edcd into bioconda:master Dec 14, 2018
@druvus druvus deleted the perl-test-pod-coverage-2 branch December 14, 2018 15:28
bgruening pushed a commit that referenced this pull request Dec 18, 2018
* Update intarna to 2.3.1 (#12367)

* Update agfusion to 1.231 (#12366)

* Update bioconda-utils to 0.15.0 (#12359)

* Update mapdamage2 to 2.0.9 (#12358)

* Update scanpy to 1.3.4 (#12357)

* Update goatools to 0.8.11 (#12361)

* Update perl-math-random-mt-auto to 6.23 (#12362)

* Update kipoi to 0.6.3 (#12374)

* Update kipoi_veff to 0.2.1 (#12364)

* Update perl-object-insideout to 4.05 (#12380)

* Update sevenbridges-python to 0.17.1 (#12379)

* Update nanosv to 1.2.3 (#12378)

* Update starfish to 0.0.30 (#12368)

* Update clust to 1.8.10 (#12356)

* Update pypairs to 2.0.6 (#12381)

* Update khmer to 3.0.0a2 (#12360)

* Update flashlfq to 0.1.110 (#12385)

* Update perl-algorithm-cluster to 1.57 (#12384)

* Update arvados-python-client to 1.2.0.20181121194423 (#12382)

* Update avro-cwl to 1.8.9 (#12355)

* Update avro-cwl to 1.8.9

* Set noarch: python

* r-breakaway (#12386)

* R sads (#12388)

* Update python-sortedcontainers to 2.1.0 (#12383)

* r-ebimetagenomics (#12339)

* pin armadilo on major version (#12389)

* IgDiscover version 0.11 (#12351)

* IgDiscover version 0.11

* IgDiscover requires Python 3.6

* Fix build on macOS with a small patch

* Remove unneeded host dependencies

* Update goatools to 0.8.12 (#12391)

* Update bioconda-utils to 0.15.1 (#12390)

* R ebimetagenomics (#12393)

* Add dimspy recipes for reference purposes (#12387)

* Add dimspy recipes for reference purposes

* Remove filename

* remove from blacklist

* Update build-fail-blacklist

* Added BioExcel_SeqQC to bioconda-recipes (#12276)

* PacBio: Update pbalign to 0.3.2 (#12396)

* PacBio: Update pbalign to 0.3.2

Closes: PacificBiosciences/pbbioconda#39

* add bgreat to bioconda (#12350)

* bgreat addition

* zlib in build should not be needed

* btrim integration to conda (#12395)

* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)

* PacBio: Update `pbsv2` to version 2.1.0 (#12400)

* Genenotebook v0.1.11 (#12398)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* prosolo: new package version 0.6.0 (#12397)

* Update sevenbridges-python to 0.17.2 (#12404)

* Add recipe for ICED (#12406)

* Downgrade version for iced (#12409)

* Update recipe for libstatgen 1.0.5 (#12348)

* Add recipe for libstatgen-1.0.5

* Update iced to 0.5.0 (#12411)

* Update perl-test2-suite to 0.000116 (#12412)

* fix compatibility with other tools (#12415)

* Restore dexseq python helper scripts (#12352)

* Restore dexseq python helper scripts

* Add python requirement for helper scripts

* Add python noarch to build section

* pin it to python2k

* Add htseq requirement, support only python <3 for now

* Genenotebook v0.1.12 (#12418)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* v0.1.12

* updated source

* added medpy recipe (#12417)

* added medpy recipe

* removed osx from build

* Update meta.yaml

* Update meta.yaml

* add boost and a compiler

* Update meta.yaml

* Update meta.yaml

* add itk

* Updated ddrage to version 1.6.1. (#12421)

* Add r-mcpcounter recipe.  (#12261)

* Add MCPcounter recipe.

* fix lint: remove 'fn'

* fix license_file, version number and doi

* Update DEXSeq requirements to force compatible HTSeq version (#12423)

* ARB: Pin glib (#11782)

* Pin glib

* Update meta.yaml

* Update meta.yaml

* Work around CB3 issues

* Work around bioconda-utils lint false positive

* Disable lint check should_not_be_noarch

* Can't reference other packages built in recipe from anything but run

* Move perl to host section. Maybe that helps.

* constraining interpreter version breaks with CB3?

* disable perl version constraint :(

* Update meta.yaml (#12426)

* stacks: fix for fix 'fixing' @ in exe_path (#12420)

* stacks: fix for fix 'fixing' @ in exe_path

the previous fix #11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- append a / to the empty string and (i.e. the bin path gets /binary)
- check for file presence (problem: neither binary nor /binary are
  present)

Now I quote the @ in the exe_path.

* stacks: add refmap bugfix

* Genenotebook v0.1.13 (#12424)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* v0.1.12

* updated source

* v0.1.13

* metaQuantome (#12413)

replaces metaquant, which is now deprecated.

* New MMseqs2 release 7-4e23d (#12432)

New mmseqs2 release 7-4e23d

* update spades to 3.13.0 (#12408)

* update spades to 3.13.0

* spades: removed dipspades; added 3.12.0 recipe in subdir

* bumped build number for 3.11.1 due to CI failure

* Update Crossmap to 0.3.1 (#12439)

* Update Crossmap to 0.3.1

* Make metaquantome dependencies more specific (#12442)

* less stringent deps

* bump build

* pin goatools

* test extra pins

* integration of bcool to bioconda (#12422)

* Update hifive to 1.5.7 (#12433)

* Update scvi to 0.2.3 (#12434)

* Update Subread from 1.6.2 to 1.6.3. (#12425)

* Update Subread from 1.6.2 to 1.6.3.

* Subread executable coverageCount has been removed.

https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ

* UCSC Cell Browser 0.4.23 (#12347)

* Starting files for ucsc-cell-browser

* Customised recipe for ucsc-cell-browser

* meta update for ucsc-cell-browser

* Changes cbTrackHub to cbHub

* Point to static release

* Moves to 0.25

* Updates sha hash for ucsc-browser

* Reverts to 0.1.9

* At ebi

* Update meta.yaml

* pins numpy to last know working version

* Back to 0.25, no numpy pinning.

* Remove git, pin python and numpy. Add build section.

* Update meta.yaml

* Update meta.yaml

* Move to 0.4.20 without skeleton on provisional commit

* Typo on executable name

* Moves to release version and adds dependencies for converters

* Update libstatgen to 1.0.14 (#12437)

* Update arvados-python-client to 1.2.1 (#12438)

* Update tirmite to 1.1.3 (#12435)

* Bump metaquantome (#12449)

* less stringent deps

* bump build

* pin goatools

* test extra pins

* bump metaquantome to 0.99.3

* Update ADAM to 0.25.0 (#12445)

* Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453)

* update rgi4.2.2 recipe (#12282)

* update to enforce python3.6 and load card.json

* remove lines from build.sh

* update build number

* make PR comment changes

* add test to verify db is loaded

* update build script

* update build script

* fix lint errors

* fix linting errors

* fix liniting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* revert test change

* Add CRAN R package leapp. (#12428)

* Bump DECIPHER to Bioconductor 3.7 (#12463)

* Bump DECIPHER to Bioconductor 3.7

* Change r-rsqlite version dependency

* Update meta.yaml

* updated scVI to 0.2.3 (#12429)

* Add recipe for PyAAVF 0.1.0 (#12451)

* Add recipe for PyAAVF 0.1.0

* Fix linting error

* seqkit 0.9.3 (#12455)

* HTSeq - Pin numpy version (#12467)

* update eigensoft to 7.2.1 (#12469)

* Update scnic to 0.6.0 (#12436)

* Update scnic to 0.6.0

* Work around fastspar insufficient armadillo pin

* fix pin

* GimmeMotifs 0.13.1 (#12471)

* Bumped version to newest, with introspective text (#12461)

* Update Segway 2.0.2 recipe to use older depedencies (#11803)

* Update Segway 2.0.2 recipe to use older depedencies

* Update maximum genomedata version supported

* Update build number

* Fix missing older dependency information

* Update meta.yaml

* updating dependencies for reparation_blast (#12443)

* updating dependencies for reparation_blast

* changed dependency of pysam

* Added DropletUtils package (#12448)

* Create recipe for SVIM (#12272)

* add svim recipe

* fix bugs in svim recipe

* replace source file

* remove license file

* Lowercase biopython

* upgrade to svim 0.4.1

* add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency

* fix python version

* try to fix lint error

* replace "skip: True" with "noarch: python"

* Update bioconductor-biocgenerics (#12477)

* [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [X] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* Irida sistr results 0.6.0 (#12478)

* Update irida-sistr-results to 0.6.0

* Fixed dependency string

* Adding recipe for clinvar-tsv v0.1.0. (#12481)

* no fixed boost version (#12483)

* New recipe: pysradb (#12470)

* Pyseer 1.2.0 (#12444)

* Update pyseer to 1.1.2

* Update pyseer to 1.2.0

* Update pyseer to 1.2.0

Update pyseer to 1.2.0

Update pyseer to 1.2.0 (fixed)

* Final touches to pyseer 1.2.0

* Additional update to pyseer recipe

* sentieon: minor version bump to 201808.01 (#12480)

* adding java to mutations recipe (#12485)

* Update ncrf to 1.00.06 (#12369)

* Update ncrf to 1.00.06

* Update test string

* Bump umitools (#12486)

* Mob suite version 1.4.9 no arch build number 2 (#12479)

* Updated to version 1.4.9

* Downgraded to python >= 3.4 to accomodate lowandrew request

* new build

* no arch commit for python 3.4

* no arch conda package version

* Set build number to 1

* Update r-goeveg to 0.4.2 (#12375)

* Update r-goeveg to 0.4.2

* Add r-hmisc as dependency

* Removes r-seurat-scripts from blacklisting (#12489)

* Removes r-seurat-scripts from blacklisting

* Unblacklist some non bioconductor packages

* For VarDict-Java, install utility scripts. (#12488)

* For VarDict-Java, install utility scripts.

Utility script that were previously only shipped with VarDict are not
part of VarDict-Java as well, making installation of both packages
unnecessary.

* Bump build.

* Improve variable name.

* Make vardict depend on vardict-java for utility scripts.

* Pin compatible numpy for older HTSEQ versions (#12490)

* Pin compatible numpy for older HTSEQ versions

This is required to keep older versions of HTSEQ functional

* HTSeq - update old versions to build properly with new build system

* HTSeq 0.6.1 - Increment build number

* add recipe for r-epic (#12473)

* Add new recipe - RVTESTS (#12465)

* Add rvtests

* Update pre-req

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Create LICENSE

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Create run_test.sh

* Update meta.yaml

* Delete run_test.sh

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Adding recipe for var-agg v0.1.0 (#12482)

* Adding recipe for var-agg v0.1.0

* runtime deps do have run-exports defined

* move rust into the host section

* Adding dependency to clangdev

* Adding var-agg v0.1.1. (#12495)

* [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441)

Salmon v0.12.0 --- version bump and fix OSX build

* Considerable updates in terms of features and fixes (check release notes).
* Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX).

* Performancean alytics (#12498)

* Add bioconductor package RNASeqR

* Add performanceanalytics

* Performancean alytics (#12499)

* Add bioconductor package RNASeqR

* Add performanceanalytics

* Move recipes/r-performanceanalytics and add r-rafalib

* Move r-performanceanalytics/ to recipes

* Update recipes/r-performanceanalytics

* Update r-rafalib

* Remove recipes/r-performanceanalytics/bld.bat

* Remove recipes/r-performanceanalytics

* Update r-performanceanalytics/

* Update r-performanceanalytics/

* Add r-performanceanalytics/

* remove r-performanceanalytics

* Add performanceanalytics

* Remove r-performanceanalytics

* Update Picard to 2.18.20. (#12501)

* Update vsearch to 2.10.0. (#12504)

* Update Purge Haplotigs to v1.0.4 (#12497)

* Update duphold to 0.1.1 (#12516)

* Update starfish to 0.0.31 (#12515)

* Update perl-term-app-roles to 0.02 (#12512)

* Update perl-dbd-sqlite to 1.60 (#12511)

* Update perl-json to 4.00 (#12509)

* Update kipoi to 0.6.5 (#12508)

* Update illumina-interop to 1.1.8 (#12507)

* Update beagle-lib to 3.1.2 (#12523)

* Update pysradb to 0.3.0 (#12522)

* Update bioconda-utils to 0.15.2 (#12525)

* Update perl-json-pp to 4.0 (#12524)

* Update perl-term-table to 0.013 (#12529)

* Update abyss to 2.1.5 (#12528)

* Update perl-test2-suite to 0.000117 (#12527)

* Update wtforms-alchemy to 0.16.8 (#12505)

* Update perl-carp-clan to 6.07 (#12518)

* Update perl-date-manip to 6.75 (#12519)

* Update: seq2c, multiqc-bcbio (#12533)

* tracy v0.3.7 (#12534)

* Version bump 2.10 (#12535)

* Version bump 2.10

* Copy paste error forgot the https

* Missing deps for ucsc-cell-browser 0.4.23 (#12537)

* Missing deps for ucsc-cell-browser

* Bumps build nuber

* Update vsearch to 2.10.1 (#12540)

* New recipe for MicroHapDB 0.2 (#12531)

* New recipe for MicroHapDB 0.2

* Troubleshoot config

* Successful build locally!

* Clean up recipe

* Update moff to 2.0.2 (#12539)

* Update PopDel to version 1.0.5 (#12502)

* Update PopDel to version 1.0.5

* Remove Makefile.patch

Remove Makefile.patch and adapt build.sh to set the correct version, date and CXX-path in its stead.

* Automatically get version from PKG_VERSION

* Update to teloclip v0.0.3 (#12542)

* Update biolite to 1.2.0 (#12544)

* Update kneaddata to 0.7.2 (#12543)

* snakemake 5.3.1 (#12500)

* snakemake 5.3.1

* fix jinja variables

* only warn if git not present in tests

* use explicit jinja for version again.

Conda seems to have lost the ability to use PKG_VERSION in meta.yaml.

* try masking env var

* try defining env var before command

* nextflow: pin openjdk=8 to solve java version parsing issue (#12493)

* Pin openjdk=8

* Alllow openjdk 8 or 9

* Update bioconda-utils to 0.15.3 (#12546)

* Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590 (#12549)

* Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590

* Update install patch for 0.2.4

* Match nim release version 0.19.0

* Scanpy scripts (#12551)

* Bump version

* Fix scanpy version requirement to v1.3.2

* Update to v0.0.4

* Update nanosim to 2.2.0 (#12517)

* Update nanosim to 2.2.0

* Add sklearn as dependency

* Recipe for kma (#12554)

* PacBio: Update `pbsv2` to version 2.1.1 (#12556)

* Add counterr (#12541)

* Add counterr

* Fix typo

* Use tagged release

* Updated ddRAGE to version 1.6.3 (#12557)

* Add recipe for SNVer 0.5.3 (#12265)

* Add recipe for SNVer 0.5.3

* Add CRAN R package cate. (#12562)

* r-seurat-scripts: Fixed DimPlots() issues, addressed libpng issue for OSX (#12563)

* Fixed DimPlots() issues, addressed libpng issue for OSX

* Correction: removed testing line in source package

* Update scanpy to 1.3.5 (#12571)

* Update vsearch to 2.10.2 (#12579)

* Update mentalist to 0.2.4 (#12578)

* Update krakenuniq to 0.5.5 (#12575)

* Update mlst to 2.16 (#12572)

* Update transit to 2.3.3 (#12570)

* Update anndata to 0.6.14 (#12568)

* Update svim to 0.4.2 (#12566)

* Update perl-test-cleannamespaces to 0.24 (#12569)

* uptdate mlst to 2.16.1 (#12582)

* Update jcvi to 0.8.12 (#12574)

* add cromwell-tools (CLI and API for Cromwell workflow manager). (#12564)

* added cromwell-tools

* point to stable docs rather than latest

* Remove noarch to make os-specifics work (#12583)

* prosolo: update to v0.6.1 (#12584)

* integration to bioconda (#12456)

* Recipe for sparcc (#12459)

* Recipe for SparCC

* Remove maintainers lines

* Add license info

* Mention pull request for patch

* Fix lint

* Build noarch

* Update: bcbio (v1.1.2), bcbio-vm (GCP support) (#12585)

* t-coffee 12.00.7fb08c2 (#12594)

* t-coffee 12.00.7fb08c2

* add viennarna to deps

Adding viennarna to runtime dependencies will include RNAplfold thus allowing -mode rcoffee to run.

* t-coffee 12.00.7fb08c2 (2)

This commit adds vienna packages
and remove TMalign copy command

* t-coffee 12.00.7fb08c2 (4)

Adding TMalign

* Nf core V 1.4  (#12599)

* Need to update SHA256 once release is out!

* Update to release 1.4

* Sleuth unblacklist (#12591)

* remove sleuth from blacklist

* Remove obsolete dependency.

* Bump spectra-cluster-cli (#12598)

* Update gseapy to 0.9.9 (#12530)

* Update gseapy to 0.9.9

* Add scipy

* Add bioservices as dependency

* added recipe perl-bio-viennangs 0.19.2 (#12596)

* Add SVMlight  (#12595)

* Add SVMlight

* Update meta yaml

* Update SHA256 sum

* Update build script to copy executables

* Update meta.yaml

* Fix o-umlaut

* Fix test stalls

svm_learn -? displays a pager, waiting for keyboard input

* rhdf5 2.26 and rhdf5lib 1.4 (#12597)

* rhdf5 2.26 and rhdf5lib 1.4

* force C99 mode

* set CFLAGS in Makevars

* Add recipe for hiddenDomains (#12614)

* bump pysradb 0.3.0 -> 0.4.0 (#12612)

* bump pysradb 0.3.0 -> 0.4.0

* Fix imports

* Add extras

* Update slicedimage to 1.0.2 (#12609)

* Update perl-module-scandeps to 1.26 (#12608)

* Update scanpy to 1.3.6 (#12605)

* Update abeona to 0.40.2 (#12602)

* Update confindr to 0.4.8 (#12607)

* Update anndata to 0.6.15 (#12606)

* tmaling (#12588)

Add tmalign recipe

* pysvmlight added (#12617)

* Add fontconfig / ttf-dejavu to fastqc recipe (#12616)

* pdate adVNTR to 1.2.0 (#12613)

* add adVNTR

* fix linux error for adVNTR

* add numpy to adVNTR requirements

* add numpy include dirs for cythonize

* Update advntr to 1.1.0

* Update advntr to 1.1.0

* update advntr to 1.1.1

* update adVNTR to 1.2.0

* update sha256 for adVNTR-1.2.0

* fix build script for adVNTR-1.2.0

* fix adVNTR-1.2.0

* PeptideShaker v1.16.36 & SearchGUI v3.3.10 (#12620)

* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6

* PeptideShaker updated to v1.16.35

* SearchGUI updated to v3.3.9

* PeptideShaker version updated to 1.16.36
SearchGUI version updated to 3.3.10

* New recipe (refinem: 0.0.24) (#12628)

* Replace sha256 and bump build num (#12629)

* Update galaxy-parsec to 1.0.6 (#12634)

* Add recipe for SeqMap (#12615)

* Add recipe for SeqMap

* Change cp

Change cp

* Updated concoct to version 1.0.0 (#12600)

* Updated concoct to version 1.0.0

* Skip build for macosx at this point

* New build number

* Reset build number to 0, thanks @druvus

* Update deepvariant to 0.7.2 (#12638)

* Update abeona to 0.41.1 (#12637)

* Update shmlast to 1.3 (#12636)

* Update krakenuniq to 0.5.6 (#12633)

* Update selene-sdk to 0.2.0 (#12632)

* Update comet-ms to 2018013 (#12555)

* Update with selene-sdk v0.2.0 (#12631)

* update with selene-0.2.0

* Update meta.yaml

* add self to recipe maintainers

* Cat updated version (#12587)



* v 4.3.1

* Pin BLAST+ version to >= 2.2, < 2.4 (#12639)

* Shmlast v1.4 (#12645)

* Bump shmlast to v1.4

* Update PopDel to version 1.0.6 (#12644)

* Update PopDel to version 1.0.6

* Adapt tests

* Remove test for correct version number

Redirection seems to cause error in circleci:
".Passing program arguments as a string may be a security hazard if combined with untrusted input"

* Concoct add samtools as a dependency (#12642)

* Updated concoct to version 1.0.0

* Skip build for macosx at this point

* New build number

* Reset build number to 0, thanks @druvus

* Samtools new requirement for concoct v1.0.0

* Bump topas (#12618)

* Bump spectra-cluster-cli

* Bump topas

* Use ${PKG_VERSION}

* Small tweaks

* No recursion

* pasta-1.7.8-build-2 (#12641)

* pasta-1.7.8-build-2

* Relax requirements

* Rebuild pasta (#12648)

* Bump spectra-cluster-cli

* Delete old pasta

* Rebuild pasta

* Unblacklist pasta

* Revert dendropy version

* Correct build number

* Use openjdk

* Rebuild perl-pod-coverage (#12652)

* Rebuild perl-pod-coverage

* Unblacklist

* tracy v0.3.8 (#12651)

* Kalign (#12647)

* add kalign

This recipe adds kalign

* fix for osx

* fix for osx #2

* Rebuild perl-test-pod-coverage (#12654)

* Rebuild perl-test-pod-coverage

* Unblacklist

* Update: bcbio (1.1.3a) Fixes bcbio/bcbio-nextgen#2594 (#12655)

* Rebuild perl-test-file-contents (#12649)

* Bump spectra-cluster-cli

* Rebuild perl-test-file-contents

* Kleborate 0.3.0 (#12657)

* Adding recipe for >> kleborate <<

* Rebuild perl-params-coerce (#12660)

* Upgrade biodb to version 1.2.0b. (#12663)

* Add recipe for unitas (#12658)

* Add recipe for unitas

* Rebuild perl-file-share (#12661)

* Update sevenbridges-python to 0.17.3 (#12667)

* Update slicedimage to 1.0.3 (#12666)

* Update cat to 4.3.3 (#12665)

* Update crossmap to 0.3.2 (#12664)

* Update: deepvariant 0.7.2 model and dependencies (#12672)

- Requires tensorflow 1.12
- Update model data for 0.7.2
- Remove requirement for --regions in dv_make_examples.py wrapper. Fixes #12560

* unblacklist perl-bio-viennangs (#12643)

* unblacklist perl-bio-viennangs

* fix version string; remove 0.19 recipe

* remove all perl version strings

* increased build nr

* Add pysvmlight (#12673)

* Remove the mess I created in the main repository (#12674)

* Add missing dependencies and bump version for FRED2 (#12621)

* Add missing dependencies and bump version for FRED2

* Bump version to force rebuild

* Update meraculous to 2.2.6 (#12254)

* Update meraculous to 2.2.6

* Remove perl pinning

* Update BioExcel_SeqQC to 0.6 (#12604)

* Update BioExcel_SeqQC to 0.6

* Fix name

* Update anndata to 0.6.16 (#12676)

* Update pysradb to 0.4.2 (#12675)

* version 3.0.3 (#12678)

* Add perl-math-utils (#12681)

* Add perl-math-utils

* Remove fn

* Rebuild perl-extutils-makemaker (#12680)

* Update perl-html-formatter to 2.16 (#12225)

* Update perl-html-formatter to 2.16

* Fix deps

* Update perl-readonly to 2.05 (#12153)

* Update perl-readonly to 2.05

* Fix deps

* Update perl-html-tidy to 1.60 (#12187)

* Update perl-html-tidy to 1.60

* Update deps

* Update meta.yaml

* Update perl-libwww-perl to 6.36 (#12180)

* Update perl-libwww-perl to 6.36

* Update deps

* Update meta.yaml

* Add perl-html-parser as dep

* Add back perl-ntlm

* Update PopDel to version 1.0.7 (#12685)

* Use quotes when extending PATH. (#12662)

* Use quotes when extending PATH env var, in order to handle potential space characters.

* Update perl-math-derivative to 1.01 (#12158)

* Update perl-math-derivative to 1.01

* Update dependency

* Update perl-data-dumper to 2.173 (#12224)

* Update perl-parallel-forkmanager to 2.02 (#12170)

* Update perl-parallel-forkmanager to 2.02

* Update deps

* Update bioblend to 0.12.0 (#12687)

* Update abeona to 0.42.0 (#12686)

* blacklist r-rbamtools
dpryan79 added a commit that referenced this pull request Aug 18, 2019
* add gsl

* try to build mzr

* add sklearn as deps

* Various updates (#12677)

* remove mzr dependent packages from blacklist

* add extended base image

* update version

* add openblas

* Use quotes when extending PATH. (#12662)

* Use quotes when extending PATH env var, in order to handle potential space characters.

* trigger

* [BULK] Fix bulk (#12695)

* Update intarna to 2.3.1 (#12367)

* Update agfusion to 1.231 (#12366)

* Update bioconda-utils to 0.15.0 (#12359)

* Update mapdamage2 to 2.0.9 (#12358)

* Update scanpy to 1.3.4 (#12357)

* Update goatools to 0.8.11 (#12361)

* Update perl-math-random-mt-auto to 6.23 (#12362)

* Update kipoi to 0.6.3 (#12374)

* Update kipoi_veff to 0.2.1 (#12364)

* Update perl-object-insideout to 4.05 (#12380)

* Update sevenbridges-python to 0.17.1 (#12379)

* Update nanosv to 1.2.3 (#12378)

* Update starfish to 0.0.30 (#12368)

* Update clust to 1.8.10 (#12356)

* Update pypairs to 2.0.6 (#12381)

* Update khmer to 3.0.0a2 (#12360)

* Update flashlfq to 0.1.110 (#12385)

* Update perl-algorithm-cluster to 1.57 (#12384)

* Update arvados-python-client to 1.2.0.20181121194423 (#12382)

* Update avro-cwl to 1.8.9 (#12355)

* Update avro-cwl to 1.8.9

* Set noarch: python

* r-breakaway (#12386)

* R sads (#12388)

* Update python-sortedcontainers to 2.1.0 (#12383)

* r-ebimetagenomics (#12339)

* pin armadilo on major version (#12389)

* IgDiscover version 0.11 (#12351)

* IgDiscover version 0.11

* IgDiscover requires Python 3.6

* Fix build on macOS with a small patch

* Remove unneeded host dependencies

* Update goatools to 0.8.12 (#12391)

* Update bioconda-utils to 0.15.1 (#12390)

* R ebimetagenomics (#12393)

* Add dimspy recipes for reference purposes (#12387)

* Add dimspy recipes for reference purposes

* Remove filename

* remove from blacklist

* Update build-fail-blacklist

* Added BioExcel_SeqQC to bioconda-recipes (#12276)

* PacBio: Update pbalign to 0.3.2 (#12396)

* PacBio: Update pbalign to 0.3.2

Closes: PacificBiosciences/pbbioconda#39

* add bgreat to bioconda (#12350)

* bgreat addition

* zlib in build should not be needed

* btrim integration to conda (#12395)

* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)

* PacBio: Update `pbsv2` to version 2.1.0 (#12400)

* Genenotebook v0.1.11 (#12398)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* prosolo: new package version 0.6.0 (#12397)

* Update sevenbridges-python to 0.17.2 (#12404)

* Add recipe for ICED (#12406)

* Downgrade version for iced (#12409)

* Update recipe for libstatgen 1.0.5 (#12348)

* Add recipe for libstatgen-1.0.5

* Update iced to 0.5.0 (#12411)

* Update perl-test2-suite to 0.000116 (#12412)

* fix compatibility with other tools (#12415)

* Restore dexseq python helper scripts (#12352)

* Restore dexseq python helper scripts

* Add python requirement for helper scripts

* Add python noarch to build section

* pin it to python2k

* Add htseq requirement, support only python <3 for now

* Genenotebook v0.1.12 (#12418)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* v0.1.12

* updated source

* added medpy recipe (#12417)

* added medpy recipe

* removed osx from build

* Update meta.yaml

* Update meta.yaml

* add boost and a compiler

* Update meta.yaml

* Update meta.yaml

* add itk

* Updated ddrage to version 1.6.1. (#12421)

* Add r-mcpcounter recipe.  (#12261)

* Add MCPcounter recipe.

* fix lint: remove 'fn'

* fix license_file, version number and doi

* Update DEXSeq requirements to force compatible HTSeq version (#12423)

* ARB: Pin glib (#11782)

* Pin glib

* Update meta.yaml

* Update meta.yaml

* Work around CB3 issues

* Work around bioconda-utils lint false positive

* Disable lint check should_not_be_noarch

* Can't reference other packages built in recipe from anything but run

* Move perl to host section. Maybe that helps.

* constraining interpreter version breaks with CB3?

* disable perl version constraint :(

* Update meta.yaml (#12426)

* stacks: fix for fix 'fixing' @ in exe_path (#12420)

* stacks: fix for fix 'fixing' @ in exe_path

the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- append a / to the empty string and (i.e. the bin path gets /binary)
- check for file presence (problem: neither binary nor /binary are
  present)

Now I quote the @ in the exe_path.

* stacks: add refmap bugfix

* Genenotebook v0.1.13 (#12424)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* v0.1.12

* updated source

* v0.1.13

* metaQuantome (#12413)

replaces metaquant, which is now deprecated.

* New MMseqs2 release 7-4e23d (#12432)

New mmseqs2 release 7-4e23d

* update spades to 3.13.0 (#12408)

* update spades to 3.13.0

* spades: removed dipspades; added 3.12.0 recipe in subdir

* bumped build number for 3.11.1 due to CI failure

* Update Crossmap to 0.3.1 (#12439)

* Update Crossmap to 0.3.1

* Make metaquantome dependencies more specific (#12442)

* less stringent deps

* bump build

* pin goatools

* test extra pins

* integration of bcool to bioconda (#12422)

* Update hifive to 1.5.7 (#12433)

* Update scvi to 0.2.3 (#12434)

* Update Subread from 1.6.2 to 1.6.3. (#12425)

* Update Subread from 1.6.2 to 1.6.3.

* Subread executable coverageCount has been removed.

https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ

* UCSC Cell Browser 0.4.23 (#12347)

* Starting files for ucsc-cell-browser

* Customised recipe for ucsc-cell-browser

* meta update for ucsc-cell-browser

* Changes cbTrackHub to cbHub

* Point to static release

* Moves to 0.25

* Updates sha hash for ucsc-browser

* Reverts to 0.1.9

* At ebi

* Update meta.yaml

* pins numpy to last know working version

* Back to 0.25, no numpy pinning.

* Remove git, pin python and numpy. Add build section.

* Update meta.yaml

* Update meta.yaml

* Move to 0.4.20 without skeleton on provisional commit

* Typo on executable name

* Moves to release version and adds dependencies for converters

* Update libstatgen to 1.0.14 (#12437)

* Update arvados-python-client to 1.2.1 (#12438)

* Update tirmite to 1.1.3 (#12435)

* Bump metaquantome (#12449)

* less stringent deps

* bump build

* pin goatools

* test extra pins

* bump metaquantome to 0.99.3

* Update ADAM to 0.25.0 (#12445)

* Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453)

* update rgi4.2.2 recipe (#12282)

* update to enforce python3.6 and load card.json

* remove lines from build.sh

* update build number

* make PR comment changes

* add test to verify db is loaded

* update build script

* update build script

* fix lint errors

* fix linting errors

* fix liniting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* revert test change

* Add CRAN R package leapp. (#12428)

* Bump DECIPHER to Bioconductor 3.7 (#12463)

* Bump DECIPHER to Bioconductor 3.7

* Change r-rsqlite version dependency

* Update meta.yaml

* updated scVI to 0.2.3 (#12429)

* Add recipe for PyAAVF 0.1.0 (#12451)

* Add recipe for PyAAVF 0.1.0

* Fix linting error

* seqkit 0.9.3 (#12455)

* HTSeq - Pin numpy version (#12467)

* update eigensoft to 7.2.1 (#12469)

* Update scnic to 0.6.0 (#12436)

* Update scnic to 0.6.0

* Work around fastspar insufficient armadillo pin

* fix pin

* GimmeMotifs 0.13.1 (#12471)

* Bumped version to newest, with introspective text (#12461)

* Update Segway 2.0.2 recipe to use older depedencies (#11803)

* Update Segway 2.0.2 recipe to use older depedencies

* Update maximum genomedata version supported

* Update build number

* Fix missing older dependency information

* Update meta.yaml

* updating dependencies for reparation_blast (#12443)

* updating dependencies for reparation_blast

* changed dependency of pysam

* Added DropletUtils package (#12448)

* Create recipe for SVIM (#12272)

* add svim recipe

* fix bugs in svim recipe

* replace source file

* remove license file

* Lowercase biopython

* upgrade to svim 0.4.1

* add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency

* fix python version

* try to fix lint error

* replace "skip: True" with "noarch: python"

* Update bioconductor-biocgenerics (#12477)

* [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [X] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* Irida sistr results 0.6.0 (#12478)

* Update irida-sistr-results to 0.6.0

* Fixed dependency string

* Adding recipe for clinvar-tsv v0.1.0. (#12481)

* no fixed boost version (#12483)

* New recipe: pysradb (#12470)

* Pyseer 1.2.0 (#12444)

* Update pyseer to 1.1.2

* Update pyseer to 1.2.0

* Update pyseer to 1.2.0

Update pyseer to 1.2.0

Update pyseer to 1.2.0 (fixed)

* Final touches to pyseer 1.2.0

* Additional update to pyseer recipe

* sentieon: minor version bump to 201808.01 (#12480)

* adding java to mutations recipe (#12485)

* Update ncrf to 1.00.06 (#12369)

* Update ncrf to 1.00.06

* Update test string

* Bump umitools (#12486)

* Mob suite version 1.4.9 no arch build number 2 (#12479)

* Updated to version 1.4.9

* Downgraded to python >= 3.4 to accomodate lowandrew request

* new build

* no arch commit for python 3.4

* no arch conda package version

* Set build number to 1

* Update r-goeveg to 0.4.2 (#12375)

* Update r-goeveg to 0.4.2

* Add r-hmisc as dependency

* Removes r-seurat-scripts from blacklisting (#12489)

* Removes r-seurat-scripts from blacklisting

* Unblacklist some non bioconductor packages

* For VarDict-Java, install utility scripts. (#12488)

* For VarDict-Java, install utility scripts.

Utility script that were previously only shipped with VarDict are not
part of VarDict-Java as well, making installation of both packages
unnecessary.

* Bump build.

* Improve variable name.

* Make vardict depend on vardict-java for utility scripts.

* Pin compatible numpy for older HTSEQ versions (#12490)

* Pin compatible numpy for older HTSEQ versions

This is required to keep older versions of HTSEQ functional

* HTSeq - update old versions to build properly with new build system

* HTSeq 0.6.1 - Increment build number

* add recipe for r-epic (#12473)

* Add new recipe - RVTESTS (#12465)

* Add rvtests

* Update pre-req

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Create LICENSE

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Create run_test.sh

* Update meta.yaml

* Delete run_test.sh

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Adding recipe for var-agg v0.1.0 (#12482)

* Adding recipe for var-agg v0.1.0

* runtime deps do have run-exports defined

* move rust into the host section

* Adding dependency to clangdev

* Adding var-agg v0.1.1. (#12495)

* [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441)

Salmon v0.12.0 --- version bump and fix OSX build

* Considerable updates in terms of features and fixes (check release notes).
* Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX).

* Performancean alytics (#12498)

* Add bioconductor package RNASeqR

* Add performanceanalytics

* Performancean alytics (#12499)

* Add bioconductor package RNASeqR

* Add performanceanalytics

* Move recipes/r-performanceanalytics and add r-rafalib

* Move r-performanceanalytics/ to recipes

* Update recipes/r-performanceanalytics

* Update r-rafalib

* Remove recipes/r-performanceanalytics/bld.bat

* Remove recipes/r-performanceanalytics

* Update r-performanceanalytics/

* Update r-performanceanalytics/

* Add r-performanceanalytics/

* remove r-performanceanalytics

* Add performanceanalytics

* Remove r-performanceanalytics

* Update Picard to 2.18.20. (#12501)

* Update vsearch to 2.10.0. (#12504)

* Update Purge Haplotigs to v1.0.4 (#12497)

* Update duphold to 0.1.1 (#12516)

* Update starfish to 0.0.31 (#12515)

* Update perl-term-app-roles to 0.02 (#12512)

* Update perl-dbd-sqlite to 1.60 (#12511)

* Update perl-json to 4.00 (#12509)

* Update kipoi to 0.6.5 (#12508)

* Update illumina-interop to 1.1.8 (#12507)

* Update beagle-lib to 3.1.2 (#12523)

* Update pysradb to 0.3.0 (#12522)

* Update bioconda-utils to 0.15.2 (#12525)

* Update perl-json-pp to 4.0 (#12524)

* Update perl-term-table to 0.013 (#12529)

* Update abyss to 2.1.5 (#12528)

* Update perl-test2-suite to 0.000117 (#12527)

* Update wtforms-alchemy to 0.16.8 (#12505)

* Update perl-carp-clan to 6.07 (#12518)

* Update perl-date-manip to 6.75 (#12519)

* Update: seq2c, multiqc-bcbio (#12533)

* tracy v0.3.7 (#12534)

* Version bump 2.10 (#12535)

* Version bump 2.10

* Copy paste error forgot the https

* Missing deps for ucsc-cell-browser 0.4.23 (#12537)

* Missing deps for ucsc-cell-browser

* Bumps build nuber

* Update vsearch to 2.10.1 (#12540)

* New recipe for MicroHapDB 0.2 (#12531)

* New recipe for MicroHapDB 0.2

* Troubleshoot config

* Successful build locally!

* Clean up recipe

* Update moff to 2.0.2 (#12539)

* Update PopDel to version 1.0.5 (#12502)

* Update PopDel to version 1.0.5

* Remove Makefile.patch

Remove Makefile.patch and adapt build.sh to set the correct version, date and CXX-path in its stead.

* Automatically get version from PKG_VERSION

* Update to teloclip v0.0.3 (#12542)

* Update biolite to 1.2.0 (#12544)

* Update kneaddata to 0.7.2 (#12543)

* snakemake 5.3.1 (#12500)

* snakemake 5.3.1

* fix jinja variables

* only warn if git not present in tests

* use explicit jinja for version again.

Conda seems to have lost the ability to use PKG_VERSION in meta.yaml.

* try masking env var

* try defining env var before command

* nextflow: pin openjdk=8 to solve java version parsing issue (#12493)

* Pin openjdk=8

* Alllow openjdk 8 or 9

* Update bioconda-utils to 0.15.3 (#12546)

* Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590 (#12549)

* Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590

* Update install patch for 0.2.4

* Match nim release version 0.19.0

* Scanpy scripts (#12551)

* Bump version

* Fix scanpy version requirement to v1.3.2

* Update to v0.0.4

* Update nanosim to 2.2.0 (#12517)

* Update nanosim to 2.2.0

* Add sklearn as dependency

* Recipe for kma (#12554)

* PacBio: Update `pbsv2` to version 2.1.1 (#12556)

* Add counterr (#12541)

* Add counterr

* Fix typo

* Use tagged release

* Updated ddRAGE to version 1.6.3 (#12557)

* Add recipe for SNVer 0.5.3 (#12265)

* Add recipe for SNVer 0.5.3

* Add CRAN R package cate. (#12562)

* r-seurat-scripts: Fixed DimPlots() issues, addressed libpng issue for OSX (#12563)

* Fixed DimPlots() issues, addressed libpng issue for OSX

* Correction: removed testing line in source package

* Update scanpy to 1.3.5 (#12571)

* Update vsearch to 2.10.2 (#12579)

* Update mentalist to 0.2.4 (#12578)

* Update krakenuniq to 0.5.5 (#12575)

* Update mlst to 2.16 (#12572)

* Update transit to 2.3.3 (#12570)

* Update anndata to 0.6.14 (#12568)

* Update svim to 0.4.2 (#12566)

* Update perl-test-cleannamespaces to 0.24 (#12569)

* uptdate mlst to 2.16.1 (#12582)

* Update jcvi to 0.8.12 (#12574)

* add cromwell-tools (CLI and API for Cromwell workflow manager). (#12564)

* added cromwell-tools

* point to stable docs rather than latest

* Remove noarch to make os-specifics work (#12583)

* prosolo: update to v0.6.1 (#12584)

* integration to bioconda (#12456)

* Recipe for sparcc (#12459)

* Recipe for SparCC

* Remove maintainers lines

* Add license info

* Mention pull request for patch

* Fix lint

* Build noarch

* Update: bcbio (v1.1.2), bcbio-vm (GCP support) (#12585)

* t-coffee 12.00.7fb08c2 (#12594)

* t-coffee 12.00.7fb08c2

* add viennarna to deps

Adding viennarna to runtime dependencies will include RNAplfold thus allowing -mode rcoffee to run.

* t-coffee 12.00.7fb08c2 (2)

This commit adds vienna packages
and remove TMalign copy command

* t-coffee 12.00.7fb08c2 (4)

Adding TMalign

* Nf core V 1.4  (#12599)

* Need to update SHA256 once release is out!

* Update to release 1.4

* Sleuth unblacklist (#12591)

* remove sleuth from blacklist

* Remove obsolete dependency.

* Bump spectra-cluster-cli (#12598)

* Update gseapy to 0.9.9 (#12530)

* Update gseapy to 0.9.9

* Add scipy

* Add bioservices as dependency

* added recipe perl-bio-viennangs 0.19.2 (#12596)

* Add SVMlight  (#12595)

* Add SVMlight

* Update meta yaml

* Update SHA256 sum

* Update build script to copy executables

* Update meta.yaml

* Fix o-umlaut

* Fix test stalls

svm_learn -? displays a pager, waiting for keyboard input

* rhdf5 2.26 and rhdf5lib 1.4 (#12597)

* rhdf5 2.26 and rhdf5lib 1.4

* force C99 mode

* set CFLAGS in Makevars

* Add recipe for hiddenDomains (#12614)

* bump pysradb 0.3.0 -> 0.4.0 (#12612)

* bump pysradb 0.3.0 -> 0.4.0

* Fix imports

* Add extras

* Update slicedimage to 1.0.2 (#12609)

* Update perl-module-scandeps to 1.26 (#12608)

* Update scanpy to 1.3.6 (#12605)

* Update abeona to 0.40.2 (#12602)

* Update confindr to 0.4.8 (#12607)

* Update anndata to 0.6.15 (#12606)

* tmaling (#12588)

Add tmalign recipe

* pysvmlight added (#12617)

* Add fontconfig / ttf-dejavu to fastqc recipe (#12616)

* pdate adVNTR to 1.2.0 (#12613)

* add adVNTR

* fix linux error for adVNTR

* add numpy to adVNTR requirements

* add numpy include dirs for cythonize

* Update advntr to 1.1.0

* Update advntr to 1.1.0

* update advntr to 1.1.1

* update adVNTR to 1.2.0

* update sha256 for adVNTR-1.2.0

* fix build script for adVNTR-1.2.0

* fix adVNTR-1.2.0

* PeptideShaker v1.16.36 & SearchGUI v3.3.10 (#12620)

* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6

* PeptideShaker updated to v1.16.35

* SearchGUI updated to v3.3.9

* PeptideShaker version updated to 1.16.36
SearchGUI version updated to 3.3.10

* New recipe (refinem: 0.0.24) (#12628)

* Replace sha256 and bump build num (#12629)

* Update galaxy-parsec to 1.0.6 (#12634)

* Add recipe for SeqMap (#12615)

* Add recipe for SeqMap

* Change cp

Change cp

* Updated concoct to version 1.0.0 (#12600)

* Updated concoct to version 1.0.0

* Skip build for macosx at this point

* New build number

* Reset build number to 0, thanks @druvus

* Update deepvariant to 0.7.2 (#12638)

* Update abeona to 0.41.1 (#12637)

* Update shmlast to 1.3 (#12636)

* Update krakenuniq to 0.5.6 (#12633)

* Update selene-sdk to 0.2.0 (#12632)

* Update comet-ms to 2018013 (#12555)

* Update with selene-sdk v0.2.0 (#12631)

* update with selene-0.2.0

* Update meta.yaml

* add self to recipe maintainers

* Cat updated version (#12587)



* v 4.3.1

* Pin BLAST+ version to >= 2.2, < 2.4 (#12639)

* Shmlast v1.4 (#12645)

* Bump shmlast to v1.4

* Update PopDel to version 1.0.6 (#12644)

* Update PopDel to version 1.0.6

* Adapt tests

* Remove test for correct version number

Redirection seems to cause error in circleci:
".Passing program arguments as a string may be a security hazard if combined with untrusted input"

* Concoct add samtools as a dependency (#12642)

* Updated concoct to version 1.0.0

* Skip build for macosx at this point

* New build number

* Reset build number to 0, thanks @druvus

* Samtools new requirement for concoct v1.0.0

* Bump topas (#12618)

* Bump spectra-cluster-cli

* Bump topas

* Use ${PKG_VERSION}

* Small tweaks

* No recursion

* pasta-1.7.8-build-2 (#12641)

* pasta-1.7.8-build-2

* Relax requirements

* Rebuild pasta (#12648)

* Bump spectra-cluster-cli

* Delete old pasta

* Rebuild pasta

* Unblacklist pasta

* Revert dendropy version

* Correct build number

* Use openjdk

* Rebuild perl-pod-coverage (#12652)

* Rebuild perl-pod-coverage

* Unblacklist

* tracy v0.3.8 (#12651)

* Kalign (#12647)

* add kalign

This recipe adds kalign

* fix for osx

* fix for osx #2

* Rebuild perl-test-pod-coverage (#12654)

* Rebuild perl-test-pod-coverage

* Unblacklist

* Update: bcbio (1.1.3a) Fixes bcbio/bcbio-nextgen#2594 (#12655)

* Rebuild perl-test-file-contents (#12649)

* Bump spectra-cluster-cli

* Rebuild perl-test-file-contents

* Kleborate 0.3.0 (#12657)

* Adding recipe for >> kleborate <<

* Rebuild perl-params-coerce (#12660)

* Upgrade biodb to version 1.2.0b. (#12663)

* Add recipe for unitas (#12658)

* Add recipe for unitas

* Rebuild perl-file-share (#12661)

* Update sevenbridges-python to 0.17.3 (#12667)

* Update slicedimage to 1.0.3 (#12666)

* Update cat to 4.3.3 (#12665)

* Update crossmap to 0.3.2 (#12664)

* Update: deepvariant 0.7.2 model and dependencies (#12672)

- Requires tensorflow 1.12
- Update model data for 0.7.2
- Remove requirement for --regions in dv_make_examples.py wrapper. Fixes #12560

* unblacklist perl-bio-viennangs (#12643)

* unblacklist perl-bio-viennangs

* fix version string; remove 0.19 recipe

* remove all perl version strings

* increased build nr

* Add pysvmlight (#12673)

* Remove the mess I created in the main repository (#12674)

* Add missing dependencies and bump version for FRED2 (#12621)

* Add missing dependencies and bump version for FRED2

* Bump version to force rebuild

* Update meraculous to 2.2.6 (#12254)

* Update meraculous to 2.2.6

* Remove perl pinning

* Update BioExcel_SeqQC to 0.6 (#12604)

* Update BioExcel_SeqQC to 0.6

* Fix name

* Update anndata to 0.6.16 (#12676)

* Update pysradb to 0.4.2 (#12675)

* version 3.0.3 (#12678)

* Add perl-math-utils (#12681)

* Add perl-math-utils

* Remove fn

* Rebuild perl-extutils-makemaker (#12680)

* Update perl-html-formatter to 2.16 (#12225)

* Update perl-html-formatter to 2.16

* Fix deps

* Update perl-readonly to 2.05 (#12153)

* Update perl-readonly to 2.05

* Fix deps

* Update perl-html-tidy to 1.60 (#12187)

* Update perl-html-tidy to 1.60

* Update deps

* Update meta.yaml

* Update perl-libwww-perl to 6.36 (#12180)

* Update perl-libwww-perl to 6.36

* Update deps

* Update meta.yaml

* Add perl-html-parser as dep

* Add back perl-ntlm

* Update PopDel to version 1.0.7 (#12685)

* Use quotes when extending PATH. (#12662)

* Use quotes when extending PATH env var, in order to handle potential space characters.

* Update perl-math-derivative to 1.01 (#12158)

* Update perl-math-derivative to 1.01

* Update dependency

* Update perl-data-dumper to 2.173 (#12224)

* Update perl-parallel-forkmanager to 2.02 (#12170)

* Update perl-parallel-forkmanager to 2.02

* Update deps

* Update bioblend to 0.12.0 (#12687)

* Update abeona to 0.42.0 (#12686)

* blacklist r-rbamtools

* just skip the check for now

* [BULK] Bulk update 191218 (#12731)

* A few updates

* update blacklist

* Fix biocsklearn

* seems to needs gsl

* fix a few recipes (#12785)

* Fixes (#12787)

* fix a few recipes

* fix recipes

* add new blacklisted recipes

* remove old recipes

* remove old recipes

* add jackstraw

* add orqa

* add isogene

* Fixes for bulk (#12788)

* fix a few recipes

* fix recipes

* add new blacklisted recipes

* remove old recipes

* remove old recipes

* add jackstraw

* add orqa

* add isogene

* add r-grain

* add r-pcalg

* fix recipes

* fix more r-* recipes

* quick fix for bulk (#12789)

* try linking the shared object

* fix dependency

* [BULK] A few fixes (#12792)

* A few fixes

* remove all bld.bat files

* build bumps

* Bulk update 241218 (#12795)

[BULK] Bulk update 241218

* increase build numbers

* bump build number

* bump

* blacklist a few more

* Bump karyoploteR as seen in https://github.com/bioconda/bioconda-recipes/pull/12732, thanks @dpryan79 and @bgruening. (#12800)

* Bulk update 271218 (#12820)

* Update atacseqqc

* another fix

* fix r-exomedepth

* update blacklist

* Fix r-loose.rock

* increase build number

* add recipes/r-rcdk to the blacklist

* various bulk fixes (#12858)

* bbn

* update the blacklist (#12862)

* various bulk updates (#12863)

* fix gviz (#12864)

* a few updates, modify blacklist (#12865)

* a few updates (#12866)

* Add a few CRAN recipes (#12867)

* Last updates for the year (#12881)

* Guten Rutsch (#12882)

* add r-diffcorr and update blacklist (#12883)

* updates for bulk (#12884)

* update and add recipes (#12885)

* Fix r-htscluster real quick

* bulk updates (#12887)

* more updates (#12888)

* more updates

* update mageckflute

* Bulk update 030119a (#12896)

* bulk updates

* a couple more updates

* Bulk updates for 040119 (#12910)

* Bulk update 040119b (#12916)

* Bulk updates for 040119

* update blacklist

* update champ

* fix license string

* bumb build number

* a few updates (#12923)

* a few updates

* Remove bld.bat

* bumb build-numbers and keep bulk busy

* bumb build-numbers and keep bulk busy (#12924)

* bump build numbers again

* a few updates (#12927)

* updates (#12930)

* updates

* Update build.sh

* Update build.sh

* build bumps and openmp

* Bulk update 060119b (#12932)

* update camera, cosmiq, and metab

* update blacklist

* fix tarball links, fix openmp problems (#12933)

* A few final fixes for OSX (#12935)

* bulk fixes

* bump

* Bump a few package versions to fix builds (#12945)

* Update blacklist (#12951)

* Update scan.upc (#12984)

* Bulk update 080119b (#12990)

* Update a few URLs and the blacklist

* Update a few more versions/URLs

* Fix bioconductor-condcomp version/URL

* Update consensus version/URL

* Update version/URL for caomicsv

* one last one

* Various package updates (#12998)

* Various package updates

* bioconductor-rnaseqpower

* more blacklisted packages

* A few last updates

* Bulk update 090119b (#13002)

* A few more updates

* Fix python in dexseq, since the count script has system requirements that aren't listed

* Update DEXSeq (#13011)

* A few updates for bulk (#13014)

* update the blacklist (#13018)

* Bulk updates (#13035)

* Bulk update 110119b (#13052)

* Various updates

* Another update

* Update flowFit

* a few updates

* Try removing a few from the blacklist (#13053)

* A few last updates to try (#13054)

* A few more updates (#13056)

* Patch bioconductor-rtandem (#13058)

* A few version updates (#13059)

* Update blacklist for packages that needed r-fda and r-compquadform (#13060)

* Bulk update 130119c (#13062)

* Update a few recipes

* These will fail

* Updates (#13064)

* Ucsc update (#13722)

* Fixed missing file PLEK.range for PLEK receipe. (#13389)

* Add new recipe for Alder (#13390)

New recipe for Alder software

* Apply fix to bash script to detect correct JAVA_HOME (#13387)

* Apply fix to bash script to detect correct JAVA_HOME

Thanks to @chapmanb for pointing to bioconda/bioconda-recipes@b726965
Thanks to @keenhl for spotting the issue

* ADd zlib to meta.yaml

* wcX: bump subversion (#13392)

* Package for vcfpy v0.12.0 (#13393)

* Update: bcbio (1.1.3 release), bcbio-vm (AWS support) (#13394)

* Update meta.yaml (#13395)

* Updates UCSC CellBrowser to version 0.4.35 (#13132)

* Bump UCSC CellBrowser to version 0.4.30

* Moves to 0.4.33 to fix versioneer cfg lack

* Update shasum 256

* Bump to 0.4.35 to sort versioneer issue.

* Add recipe for gerp++ (#13391)

* Add recipe for gerp++

* Remove r-basejump from blacklist to build it under 3.5. (#13398)

* [coprarna] bump dep perl-list-moreutils to 0.428 (#13397)

* Update ConFindr to 0.5.1 (#13401)

* Pathogist (#13145)

* Add pathogist recipe

* Change sha256

* Fixed test

* Fixed test

* build #0

* Add a proper setup.py, fix python pinning

* Right, noarch, though it's still pinned

* forgot setup.py

* Set Matplotlib to use Agg

* Fixed sha256

* Build r-bcbiobase for R 3.5 (#13402)

* gffcompare: change build.sh to use prep_linux.sh (#12407)

- this is solution suggested by the developer: https://github.com/gpertea/gclib/issues/4
- removed gffcompare as developer suggested
- removed blacklist entry

* Bump fcsparser to 0.2.0. (#13405)

* Update: CNVkit bump for failed linux build (#13403)

Previous build, which fixes CNVkit with recent pandas, failed when
building on CircleCI so doesn't have a new package. Bump build number
and re-build.

https://circleci.com/gh/bioconda/bioconda-recipes/40931

* add new recipe for MALDER software (#13406)

* Build r-bcbiornaseq for R 3.5.1 (#13404)

* Bump r-bcbiornaseq to v.2.8

* Remove r-bcbiornaseq from blacklist.

* Fix typo.

* recipe: r-misha (#13408)

* repice: r-misha

* skip osx build

* Change conda description (#13409)

* fixed type (#13410)

* GATK4: bump version (#13412)

* Update xopen to 0.5.0 (#13413)

* new packages: r-umi4c, r-shaman (#13396)

* new package: r-umi4c, r-shaman

* Igv fix (#13414)

* [*] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [*] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [*] This PR updates an existing recipe.
* [*] This PR does something else (explain below).
Updated igv to newest version, fixed broken linkt to jar file, added test

* Stacks 2.3 (#13095)

* Stacks update 2.3

* Stacks folder cleanup

* stacks remove 1.47

* nextflow 19.01.0 build 4 (#13418)

This commit changes the build script so that
it modifies the NXF_DIST directory to the package
path provided by Conda

See https://github.com/nextflow-io/nextflow/issues/954


* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* Added recipe for illumina-cleanup (#13417)

* Added recipe for illumina-cleanup

* Fixed test issue (Nextflow cache)

* updated dxpy to 0.273.0 (#13407)

* [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [X] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [X] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* add stream_chromvar recipe (#13419)

* add stream_chromvar recipe

* Add imctools (#13420)

* Add imctools

* Only actual requirements

* Update meta.yaml

* rust-bio-tools 0.2.8 (#13411)

* rust-bio-tools 0.2.8

* added clangdev

* Add starcode

* Add cxx compiler.

* explicitly use newest clang on osx.

* Perl www mechanize and dependancies (#13218)

* Add new test and dependancies

* init www-mechanize recipe

* init html-form recipe dependancy

* complete perl dependancies & fix sh

* fix perl dependancies and sh

* Add basic tests

* add more basic test

* Changing modules position...

* Updated percolator to 3.2.1 for building against boost = 1.64 (#13425)

* Fix optitype numpy requirements (#13427)

* Fix optitype numpy requirements

* Syntax fixed

* Fix numpy to 1.10

* Add prokaryote from pypi (#13428)

* Add prokaryote from pypi

* Update meta.yaml

* Update meta.yaml

* Update cgat-core to 0.5.6 (#13348)

* Try to trigger OSX build (#13429)

* srnapipe: new recipe (#13416)

* Added sRNAPipe recipe.

* Updated tool dependencies versions.

* Changed repo name

* Updated sha256

* Changed build to host

* Update IslandPath to 1.0.4 (#13421)

* Increment version

* Update sha256

* Update sha256

* Add pinned numpy dependencies (#13437)

* Update: bcbio, bcbio-vm, bcbio-variation-recall (#13435)

- bcbio: latest development version with fixes for CWL generation
- bcbio-vm: support for remote file lookup via bcbio
- bcbio-variation-recall: fixes for latest bcftools

* updated prince to 2.0 (#13434)

* Remove the cf201901 label (#13440)

* Update seqlogo meta.yaml (#13433)

* Update meta.yaml

* Update meta.yaml

* Bump deepTools and its dependencies (#13442)

* Bump deepTools and its dependencies

* fix py2bit, remove obsolete pybigwig/0.1.11

* old pysam builds don't work with python 3.7

* nimnexus v0.1.1 (#13443)

* Update meta.yaml

* Update meta.yaml

* reset build-number and test the new build-infrastrucutre

* pb-falcon: update build (#13446)

Hopefully to fix https://github.com/PacificBiosciences/pbbioconda/issues/85

* pb-assembly: update build, and specify python2 (#13447)

Hopefully to fix
https://github.com/PacificBiosciences/pbbioconda/issues/85

* samtools w/ openssl-1.1.1 (#13448)

Another attempt to deal with python2.7.15/openssl issues. E.g.
https://github.com/PacificBiosciences/pbbioconda/issues/85

Note: samtools-1.9 was built against opensll-1.0.2, which conflicts
with the latest python2.7.15 build.
openssl-1.1.1a and openssl-1.0.2p are not ABI-compatible, so we need to
specify that.

I do not see a way to pin the old opensll (since there is ambiguity
between 1.0.2o and 1.0.2p), so I am taking the suggestion
from kylebeauchamp and rebuilding with openssl-1.1.1. That might break
some people until they upgrade python, etc. but I do not
see a better solution without actually bumping the version of samtools.

* update bioconda-utils (#13445)

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* samtools w/ openssl >= 1.1.1 (#13450)

* samtools w/ openssl >= 1.1.1

See #13448

Simply rebuilding samtools did not grab the more recent openssl.
(See previous commit.)

* Trying to fix syntax error for opensll version spec

* Still trying

* Updated PyPairs to v3.0.9 (#13449)

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* pb-assembly-0.0.4: openssl-1.1.1a (#13452)

After I rebuilt samtools, the samtools problem disappeared for me in some cases,
but only because pb-assembly was suddenly using the older openssl again.

Hopefully, this will create a self-consistent tree.

* pb-assembly: bump build number (#13453)

Maybe this will cause 0.0.4 to show up. I have not seen
it since merging several hours ago.

* Update meta.yaml

* Update meta.yaml

* Updated metal.yaml for new prince release (#13454)

* chado-tools 0.2.5 (#13456)

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* cnv_facets (#13457)

* First draft

* Restrict to linux

* Add snp-pileup dependency

* Do not use setup script

If some dependency is missing, edit meta.yaml or explicitly put
dependecies build.sh

* Install without setup.sh

* Fix R command

* Move test to meta.yaml

* Fix yaml line

* Test moved to build script to resolve #38177 (upload-linux)

* Install jsonlite in build script

After installation, argparse fails as it cannot find jsonlite (?!) so we
install jsonlite explicitly.

Version bumped so the version string from cnv_facets.R -v agrees with the
release version

* Try moving jsonlite from build to meta

This to try to resolve the error occurring *after* downloading
cnv_facets:

    cnv_facets.R -h
    Error: package or namespace load failed for ‘argparse’ in
    loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
    there is no package called ‘jsonlite’
    Execution halted

* Bump buld number

* Recipe for version 0.12.0

* Update to v0.12.1

* Update to version 1.15.0

* Test using -v and use bash

* Revert to sh

* Try with zlib

* Use bash script shipped with ASCIIGenome package

* Fix sed command

* Try sending sed output to dest dir directly

* Fix symplink

* Copy - do not symlink

* Add libgfortran - fix url

* Use c compiler

* Fix shasum

* rebuild openms against new compilers (#13458)

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependants) (#13444)

* Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependants)

* Update meta.yaml

* fix checksum

why oh why does this change ...

* Try to speed up debugging of bowtie2 with new compilers

* Update build.sh

* add nucleosome prediction tool (#13455)

* [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [ ] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

what a hack ...

* Remove old bowtie2 versions from the blacklist (#13462)

* update pinning for bwa and paml (#13463)

* samtools: Do not specify openssl version (#13464)

This does not solve our problem in all cases, and it may
hinder bioconda-wide changes to the openssl version.

See https://github.com/bioconda/bioconda-recipes/pull/13448

* pb-assembly: Do not specify openssl version (#13464) (#13466)

This does not solve our problem in all cases, and it may
hinder bioconda-wide changes to the openssl version.

See https://github.com/bioconda/bioconda-recipes/pull/13448

* Update pinnings for clustalw, hmmer and pybedtools (#13467)

* Update pinnings for clustalw, hmmer, pybedtools and t_coffee

* Update recipes

* hashy hash

* t_coffee needs quite a bit of TLC, skip until later

* Feb 2019 Release (#13474)

* Feb 2019 Release (#13476)

* Feb 2019 Release (#13477)

* Feb 2019 Release (#13478)

* Feb 2019 Release (#13479)

* Add socru (#13482)

* Add socru

* Pinning updates for bamtools and seqtk. Update blacklist to… (#13483)

* Pinning updates for bamtools, bowtie1, and seqtk. Update blacklist to exclude presumably unused versions of said tools in the future

* bowtie

* add tbb-devel

* bowtie1 has code issues, I'm not going to bother

* delly v0.8.1 (#13491)

* Feb 2019 Release (#13481)

* Feb 2019 Release

* Feb 2019 Release

* revert libweb dep (#13497)

* [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [ ] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* Update xpclr (#13500)

* require python 3.6

* Update xpclr to version 1.1.1

* Add recipe for SpydrPick (#13468)

* Add recipe for SpydrPick

* Add cmake dependency

* Use git_url to clone recursively

* Recursively clone apegrunt submodule

* Correct git submodule command

* Get apegrunt through git clone

* Add TBB_ROOT to cmake command

* Try TBB_ROOT as env variable instead

* Add patch for cmake policy

* Add tbb-devel

* Correct apegrunt checkout

* Install boost accumulators

* Add boost functional

* Add pthreads

* Link libgcc statically

* Add patch to add librt to linker line

* Fix install command

* Fix test commands (help gives exit 0)

* Specific version of boost; add FindTBB.cmake to recipe

* Don't checkout whole boost git history

* Update pinning for bbmap, cutadapt, and htseq (#13492)

* Update pinning for bbmap, cutadapt, and htseq

* noarch: python

* tweak recipes, not sure what's wrong with bbmap

* Try to debug bbmap

* OK, try two additional bbmap tests

* exclude grepping for the version

* Another two tests

* Add another grep, uncomment the last non-version check

* grep Version works if I recreate things locally, I suspect this is some weird dockerized environment grep thing

* Fix bbmap

* bump rapmap to v0.6.0 (#13495)

* bump rapmap to v0.6.0

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Delete conda_build_config.yaml

Should be using the new compilers by default.

* increase version number (#13480)

* increase version number

* Update meta.yaml

* Feb 2019 Release (#13502)

* [coprarna] remove build env (#13501)

* remove build env; noarch=generic

* noarch python

* r-base 3.4.1

* undo noarch

* Feb 2019 Release (#13504)

* Feb 2019 Release (#13506)

* Build samtools 0.1.19 and update pinnings (#13505)

* Update build-fail-blacklist (#13503)

* Update build-fail-blacklist

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* use libitk

* PICRUSt2 install fix (#13173)

* Added post-link and pre-unlink scripts to correctly install database and accessory scripts

* Update meta.yaml to tag specific versions of requirements

* Bump to PICRUSt v2.1.0-b

* update stream_atac to 0.2.0 (#13469)

* update stream_atac to 0.2.0

* Added fastq_utils recipe (#13473)

* Added fastq_utils recipe

* Remove noarch

* Attempt to fix curses error for Samtools following that recipe's example

* Attempt to resolve samtools compile issue

* Simplification and use of bam.h from Conda Samtools package

* Probably futile attempt at fix

* Try adding a conda build file

* Tidy up spacing

* Small futile tweaks

* Does this work to use newer GCC?

* Reinstate buld config, bump build

* Add compiler to host

* Revert "Add compiler to host"

This reverts commit 5c01e55113237fc871eced987f7ca04ceadc88ce.

* Replace gcc call with x86_64-apple-darwin13.4.0-clang

* sed the correct Makefile, use Make variable syntax

* Attempted fix for cannot find -lz

* Hopefully LDFLAGS is what's needed

* Okay, source package doesn't use LDFLAGS, use CFLAGS to pass options

* Try with older GCC

* Oh my god it works - tidy up

* Bumped runtime samtools to 1.9, removed legacy compiler requirement

* Update sistr (#13441)

* Fixed version of blast

* Remove sistr_cmd from build blacklist

* Updated sistr file

* Changed blast version definition

* rebuild stream_atac 0.2.0 (#13509)

* update stream_atac to 0.2.0

* update stream_atac to 0.2.0

* update stream_atac to 0.2.0

* rebuild stream_atac 0.2.0

*  update stream to 0.3.4 (#13510)

* update stream to 0.3.4

* HiCExplorer: Add a dependency, add test cases, increase build number to 1 (#13424)

* Add dependency, add test cases, increase build number to 1

* rebuild some dependencies

* reset

* bump

* bl hicexplorer for the moment

* Feb 2019 Release (#13512)

* update hicexplorer (#13511)

* remove build.sh

* rebuild pygenometracks and hicexplorer

* skip py37 as long as itk is not rebuild

* make it noarch

* Feb 2019 Release No Ambertools (#13513)

* Delete post-link.sh (#13517)

* Maybe this should depend on openssl explicitly (#13518)

Maybe the whole problem was that it was being built against
system openssl. I do not see where openssl-1.1.1 is being
specified in Bioconda. In theory, we should be using 1.0.2
everywhere already.

https://github.com/conda-forge/conda-forge.github.io/issues/701

* Update: smoove 0.2.3; fix recipe, remove from blacklist (#13515)

Fixes bcbio/bcbio-nextgen#2666

* Feb 2019 Release Ambertools in post-link.sh script (#13519)

* Update Picard to 2.18.25. (#13196)

* Update Picard to 2.18.25.

* Remove Picard subdirectories for older versions.

The packages for these versions remain available; remove the
subdirectories since they keep getting rebuild on version bumps and
some of them fail to build.

* Update Picard to 2.18.26. (#13521)

* bumping LAST to 963 (#13524)

* bumping to 963

* adding zlib to dependencies

* trying adding C and LDFLAGS

* passing flags directly to make

* trying other things with make install flags

* Do I need g++, then?

* Feb 2019 Release, biopython==1.72, renaming cpptraj to biobb_cpptraj (#13522)

* sumaclust breaks nightly builds (#13516)

* ok, lets see what going on here and on the nightly builds

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* add to host as well

* CC

* Move to newer package with fixes and additions (#13526)

* Tracy (#13529)

* tracy v0.5.1

* Atlas (#13514)

* add metagenome-atlas for linux

* rapid v0.8 (#13520)

* rapid v0.8

* Update section name to host, upon bgruening s suggestion

* Removing all pinnings

* Remove r-workflowscriptscommon from blacklist (#13535)

* Updated Artemis recipe to version v18.0.2 (#13537)

* [viennarna] pkgconfig data enabled (#13536)

* [viennarna] pkgconfig data enabled

* [viennarna] bump build

* Atlas (#13532)

* correct entry point

* pymzml only for python3 (#13543)

* [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [ ] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* Update: smoove; remove tabix requirement, in htslib (#13544)

* Pinning bedtools version (#13545)

The output fields of the 'bedtools coverage' command, in combination with the parameters I've employed, has changed. That's affecting some downstream analysis. So, I preferred to pin this version for the moment.

* Fix nightly (#13546)

* Fix megagta and pymzml

* fix dinopy

* blacklist megagta, I don't know what's wrong with it and don't really care to find out

* Fix ddrage meta.yaml

* Fix gdsctools and standardize the blacklist

* All meta.yaml should have a build number

* Blacklist gdsctools, I'm not going to add tests when I don't know the tool

* one more old package to blacklist

* Update PlantCV to v3.1.0 (#13549)

* Fix piret (#13551)

* Fix piret

* bump piret

* [socru] Bump 1.0.0 (#13552)

* Bump 1.0.0

* Adding minnow (dscRNA-seq read level simulator) (#13550)

* change include path

* * added the build files for minnow

* resolved the errors for zlib

* Adding the md5 sum

* Added the build number

*     MAC OS patch added

* removed redundent packages

* removing flags

* removing flags

* md5 sum changed

* md5 sum changed

* Update gtdbtk version (#13554)

* AMPtk v1.3.0 release (#13553)

* amptk v1.3.0 update

* detab post link msg

* spaces in post-link.sh

* clean up the blacklist a bit

* Fix minnow (#13555)

* Fix build number in minnow

* md5sum

* this is probably the correct commit

* Update pinning for freebayes, salmon, sambamba and subread. Update STAR. (#13508)

* Update pinning for freebayes, salmon, sambamba and subread. Update STAR.

* freebayes is a total mess, I'm not spending all day patching it.

* add cooler 0.7.6, since some things are pinned to it.

* Fix cooler URL

* Fix cooler 0.7.6 imports

* Sambamba compilers

* Update build.sh

* add -headerpad_max_install_names

* try ldc 1.12.*

* Update meta.yaml

* HiCMatrix update to version 7 (#13557)

* Abeona: Bump nextflow version (#13561)

* pourRNA recipe (#13490)

* build script

* Create meta.yaml

* lowercase name

* add about:summary

* rebuild viennarna

* test libstdcxx-ng

* Revert "rebuild viennarna"

This reverts commit a1076c082e4ec893ca3ab8e85d7ec0caba7625e7.

* libstc++ with c++11 support

* + old lib

* test

* test2

* build 0

* without automake

* without autoreconf

* url update

* test

* key

* with prefix

* v1.0.1

* + prefix

* GPLv2

* add `make check`

Thanks for the hint @eggzilla

* pin to viennarna < 3

* summary extended

* connecting to a release (1.2) (#13563)

* change include path

* * added the build files for minnow

* resolved the errors for zlib

* Adding the md5 sum

* Added the build number

*     MAC OS patch added

* removed redundent packages

* removing flags

* removing flags

* md5 sum changed

* md5 sum changed

* fix merge error

* HiCExplorer 2.1.1 update (#13564)

* hicap recipe (#13539)

* hicap recipe

* optimize the recipe a little bit

* Delete build.sh

* trigger

* update stream to 0.3.5 (#13568)

* update stream to 0.3.5

* update stream_atac to 0.3.0 (#13569)

* update stream_atac to 0.3.0

* bump vienna_rna (#13465)

* bump vienna_rna

* remove old versions

* add run_exports

* rebuild viennarna (#13570)

* rebuild viennarna

* Update meta.yaml

* Add Perl module Text::Levenshtein (#13571)

* Add Text::Levenshtein from CPAN

* Remove dependency on Unicode::Collate

* Update meta.yaml

* Dammet (#13499)

* added dammet

* fixed installation issues

* updated dammet cmake and added dependencies

* test

* Using htslib from conda

* typo in makefile.bioconda

* updated sha256

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* added nlopt

* added a test to nlopt

* rm nlopt as already installed on conda-forge

* typo

* Update meta.yaml

* stacks: adds version 2.3b (#13538)

* stacks: adds version 2.3b

see https://groups.google.com/d/msg/stacks-users/QYW8Pd15FI8/eALNz1gqEgAJ

* Delete conda_build_config.yaml

* cnv_facets v0.13.0 (#13572)

* Upload v0.13.0

* Fix version in URL

* Remove junk from git

* [intarna] switch to boost-cpp + docu extended (#13559)

* [intarna] switch to boost-cpp + docu extended

* patch to disable VRNA pkgconfig check

* apply patch to disable VRNA version check

* Final linebreak in patch

* Disabling explicit pathes

* Undo last change

* Viennarna 2.4.9

* Update build.sh

* cxx compiler

* Delete IntaRNA.configure.noRnaVersionCheck.patch

* build with 2 cores

* cleanup

* Update: arvados-cwl-runner, arvados-python-client; py3k (#13576)

* Update: arvados-cwl-runner, arvados-python-client; py3k

* Do not build on python 3.7; ciso8601 blocking

* Try noarch to fix missing 2.7 package builds

* Try skipping python 3.7 with selectors

* Remove other noarch

* Try python 3.7 binning and not skipping osx

* Add noarch recommendation from lint

* Try adding noarch back to arvados-python-client

* update stream_atac to 0.3.1 (#13581)

* update stream_atac to 0.3.1

* Adding new to the PR template (#13579)

* Initial commit for package tango (#13567)

* Initial commit for package tango

* Update meta.yaml

* use script

* Delete build.sh

* updating cromwell to 0.37 (#13582)

* Update mz2sqlite (#13595)

* Update meta.yaml

* Update mz_to_sqlite.py

* Fmlrc update (#13612)

* updating version, sha256, and commands

* redirecting to null

* Added tximport-scripts recipe (#13585)

* Added tximport-scripts recipe

* Added dropletutils as dependency

* Remove stupid typo

* Add requested fixes

* Remove runtime R pinning

* Add bioverbs recipe (#13592)

* Add bioverbs recipe

* Bump source package version

* Remove R pinning

* Renamed dir to reflect r- prefix

* Add recipe for HLA*LA (#13573)

* Initial test commit HLA-LA

* .

* .

* .

* Initial commit

* Add Text::Levenshtein from CPAN

* Remove dependency on Unicode::Collate

* .

* Add HLA*LA

* Try reduced dependencies

* Remove jsoncpp dependency

* Full boost required.

* Update meta.yaml

* Skip OSX builds

Dependency Bio::DB::HTS not available for OSX.

* Cleaned up file

* Cleaned up file

* Use pushd/popd

* R goalie (#13596)

* Add r-goalie recipe

* Remove lines that deal with 3.4.1 issues

* Update goalie source

* [WIP] Add makefile patch, bump BWA. (#13594)

* Add makefile patch

* Try bigger patch

* Rebuild BWA 0.7.3a for GCC7 (#13617)

* Add makefile patch for BWA 0.7.3a

* Fix patch

* Try one more time to get working patch

* Add dummy commit

* R transformer (#13614)

* Added r-transformer recipe

* Version dependencies

* Remove duplicated dependency

* Adding npInv (#13608)

* changed all peptide-shaker to npinv, wonder if this works :)
* bump to v1.24, should now enable --help with return

* Update svim to 0.4.4 (#13599)

* Update GraphAligner to v1.0.3 (#13590)

* Update GraphAligner to v1.0.3

* Update: bcbio-variation-recall 0.2.3 with wrapper fix chapmanb/bcbio.variation.recall#22 (#13605)

* Update: arvados-cwl-runner, arvados-python-client; second py3k attempt (#13591)

Original noarch approach didn't work properly on py3k due to
subprocess32 conditional selector. It doesn't get applied on
noarch so will be a dependency and make it incompatible with py3.
Trying a new approach to restrict to avoid py37 errors.

* I haven't updated stuff from the WGBS pipeline yet, but this takes ca… (#13584)

* I haven't updated stuff from the WGBS pipeline yet, but this takes care of the rest of snakePipes

* Try compiling fatotwobit on OSX. If that works, the other UCSC tools can be compiled there as well.

* build remaining packages on OSX too

* omero: install bin/omero as well (#13618)

* omero: install bin/omero as well

see: https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=8678

* omero: Bump build number

* Remove setup.py after use

* Update trumicount to 0.9.13 (#13603)

* trying to fix the openjdk java version (#13622)

* Slamdunk (#13580)

* Build number updated. sha256 updated.

* R version set to 3.2.2

* Slamdunk build number set to 2.

* Trying out different R versions.

* Installing tidyverse dependency for ggplot2.

* Version 0.3.3

* Slamdunk v0.3.4

* use jinja vars

* Update meta.yaml

* Add msp2db (#13627)

* Add msp2db

* Added r-brio (#13620)

* R syntactic (#13619)

* Add r-syntactic recipe

* Version dependencies

* Feb 2019 Release (#13631)

* Update SpydrPick to v1.1.0 (#13630)

* Move to ucsc-cell-browser 0.4.38 (#13593)

* Move cellbrowser to 0.4.36, removing R dependency

* Move to 0.4.38 using pip to avoid eggs.

* Use recommendation from Bjoern for install.

* ARB - gcc7 rebuild (#13616)

* Rebuild GCC7
* Create cxxforward.patch
* Workaround broken conda-forge perl package
* Workaround missing binaries (gcc, ld, ...)
* Fix greadlink missing on macos
* Fix typeof undefined

* Frogs3.0.0 (#13000)

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

(Poke @mariabernard @oinizan )

* Isocor recipe (#13601)

Add Isocor 2.1.0

* Update r-bcbiobase recipe to pin r-basejump 0.7.2 (#13629)

* Pin to basejump v0.7.2

* Also pin run step to basejump v0.7.2

* Move r-seurat-scripts to seurat-scripts and bump version. (#13634)

Move r-seurat-scripts to seurat-scripts and bump version to 0.0.5

* Updated Basejump with newly packaged dependencies (#13632)

* [socru] Bump 1.0.1 (#13640)

Update 1.0.1

* Update fpa to 0.4 (#13644)

* snakemake 5.4.1 (#13647)

* Fix ARB run_exports (#13637)

* Update pinnings for deeptoolsintervals (#13648)

* Updating staramr (#13650)

*  update stream to 0.3.6 (#13649)

* update stream to 0.3.5

* update stream to 0.3.5

* update stream to 0.3.5

* update stream_atac to 0.3.0

* update stream_atac to 0.3.1

* update stream to 0.3.6

* rebuild stream 0.3.6

* Add draft wg-blimp-v0.9.0 (#13638)

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [x] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [ ] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

This is a first test version, things will likely change until final PR.

* update mykrobe to v0.6.1 (#13566)

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

As this is my first recipe (technically an update, but I effectively had to write from scratch as the program has changed quite a lot) it would be great to have a review from the core team.

* Rapid08 (#13652)

* v0.8 update - added r-viridis package

* r-viridis fix version

* 0.8 viridis, plots CB friendly update

* rapidv0.8_build_1

* Added pin to bowtie2 (v2.3.0) because of the issue: https://github.com/BenLangmead/bowtie2/issues/230

* PacBio: Update `ccs` to version 3.4.0 (#13651)

* Bump sniffles (#13654)

* Update wg-blimp to v0.9.1 (#13653)

Update wg-blimp to v0.9.1 (#13653)

* Rebuild infernal (#13655)

* Rebuild infernal

* Rebuild infernal

* rebuild hla*la (#13656)

:information_source:
Bioconda has finished the [GCC7 migration](https://github.com/bioconda/bioconda-recipes/issues/13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](https://github.com/bioconda/bioconda-recipes/issues/13578).

----------------

* [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [ ] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* Adding recipe for digestiflow-cli v0.4.1 (#13642)

* Update to Gromacs 2019 (#13523)

* Update to Gromacs 2019 and 2018.5
http://manual.gromacs.org/documentation/2019/download.html

* maxbin-2.2.6 (#13659)

* Update for Gromacs 2019.1 (#13660)

* Bump umis to v1.0.2. (#13664)

* Snakemake 5.4.2 (#13662)

* snakemake 5.4.1

* snakemake 5.4.2

* JBrowse 1.16.2 (#13657)

* update to 1.16.2

* patch is not needed anymore

* Tango (#13658)

* Initial commit for package tango

* Update meta.yaml

* use script

* Delete build.sh

* Bumped tango to version 0.3.0

* pb-assembly: Try openssl<1.1 (#13574)

* Add compare-reads (#13635)

* Add compare-reads

* Add python run reqs

Should be brought in by pysm, but I see this in the build logs:
```
WARNING (compare-reads,lib/python2.7/site-packages/compare_reads…
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