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Push cb3 migration directly into master (#9402)
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* bump CONDA_GSL to 2.4 (#8622)

* update limma (#8616)

* bumping groot to v0.7 (#8618)

* New: GATK4 vqsr_cnn python module (#8617)

Provides neural network based filtering for GATK4 variant calling
https://gatkforums.broadinstitute.org/gatk/discussion/10996/deep-learning-in-gatk4

* Add EMA (#8612)

* ema

* Update ema

* Update ema

* Update ema

* Add py{{ CONDA_PY }} to build string (#8611)

* bump CONDA_GSL to 2.4

* use mktemp by default in bootstrap.py (#8625)

* fix doi

* use mktemp on osx

* always use mktemp

* Added new perl-extutils-cbuilder recipe (#8619)

* Bump quasitools version to 0.3.1 (#8627)

* Add recipe for fqtrim (#8629)

* Add recipe for fqtrim 0.9.7

* Add variables

* auto bump build numbers

* attempt lint fix?

* add missing hash for gfold

* reverty fwdpy11 meta

* add openblas to all packages that didn't already include it

* bump packages except bioconductor-rmat and pymix.  the latter fails lint tests, but CI doesn't give a reason

* conda-forge seems to pin at 2.2, so I guess we should, too?

* freaky magic courtesy of @johanneskoester

* roll eqtlbma back to gsl 1.16

* pinning to 1.16 fails bioconda lint checks

* add eigensoft and ea-utils to blacklist

* attempt to build eqtlbma with GSL 1.16

* add linting exception

* add lcfit

* skip OSX for the moment

* Use cb3-migration branch and latest miniconda release.

* Check all recipes on bulk.

* remove build string (#9042)

* remove build string

* remove conda vars (#9043)

* Replace gcc with new compilers.

I always replace with the c compiler. For c++, we manually have to manually modify the line.
Anaconda upload is disabled for now, because we should check that pinning works before we start uploading.

* Fixes. Enable upload. It should be no problem, because conda-build seems to fail if host is not used for library dependencies.

* Fix version spec.

* Trigger cache update.

* Trigger cache update.

* Trigger cache update.

* Trigger cache update.

* Trigger cache update.

* add host section to python based packages with c/cxx compiler

* replace build with host

* small fixes

* small fixes

* fix spacing

* replace numpy x.x

* use pip install

* some more python changes

* minor

* host and build section for perl-data-dumper and perl-extutils-makemaker.

* small round of r recipes to check bulk building

* r-* build -> host

* temporarily disable cache

* trailing whitespace

* fix boost version specs

* temporarily disable cache, try two

* temporarily disable cache, try three

* temporarily disable cache, try four

* temporarly disable uploads for bulk branch

* add noarch python

* add build/number sections

* split into host:/build: for bioconductor packages

* c -> cxx compiler if using r-rcpp or r-cpparmadillo

* build -> host for r/bioc recipes not otherwise using cb3 build:

* trigger; try out logic for divergent build strings

* Revert "temporarly disable uploads for bulk branch"

This reverts commit 3cf5983.

* Whitespace fixes [WIP] (#9085)

* HiCExplorer version 2.1.4 (#9044)

* Adding hic2cool version 0.4.1

* Update to version 2.1.4 of HiCExplorer

* Update to asqcan v0.2 (#9047)

* Update to asqcan v0.2

* Fixed md5

* [ci skip] add doi to deeptools (#8963)

* hicexplorer fix

* Update with new dependency (#9048)

* vep: bumped subversion (#9051)

* adding illumiprocessor v2.0.9 (#9045)

* geneimpacts: bumped subversion (#9052)

* r-geoaxe, r-oai, r-rbison, r-rebird, r-ridigbio, r-rvertnet, r-wicket (#8994)

* r cran packages dependencies for rspocc and rgbif, recipes generated with skeleton. Ecology tools, for integration in Galaxy

* Rpackages for ecology

* rm win tags

* Bumped star-fusion version (#9034)

* Bumped star-fusion version
* conda considers 2.6.0b<2.6

* snpsplit : new version added (#9054)

* Mmseqs2 (#9055)

* Update MMseqs2 recipe to new release 3-be8f6

* Update r-biodb to 1.1.0. (#9057)

* OrthoFinder: update to 2.2.6 (#9060)

* Orthofinder: update to 2.2.6

* fix link

* snakemake 5.1.4

* Update BioConda pypeFLOW package to v1.0.0 (#9024)

* pypyFLOW v1.0.0

In the absense of an official tag on the upstream repository,
this is the commit which bumped the version number to 1.0.0

See PacificBiosciences/pypeFLOW#51

Note that the dependencies declared in the setup.py changed,
which is reflected in the meta.yaml dependencies. It now
requires networkx.

Also, the updated setup.py declares additional python libraries
which we now test can be imported.

* Use the merge commit for the v1.0.0 version bump.

Hat tip Renan Valieris, the version 1.0.0 bump commit
79c77235eb10e7b36a98ada891e1e6ef454aed58 was part of
a pull request which make other changes, thus merge
commit e331fad50be98d83e95a4a354bed2c81a8351392 is a
better representative of v1.0.0. See
PacificBiosciences/pypeFLOW#39

This pull request also expanded the supported range of
networkx versions.

* Remove space in networkx dependency version definition

* Bump dimspy version to 1.2.0 (#9063)

* Update to pypeFLOW v1.1.0 (#9064)

In the absense of an official tag on the upstream repository,
this is the commit which merged pull request 20 into the
master branch, and that included the version bump.

See PacificBiosciences/pypeFLOW#51

There is a new futures dependency declared in their setup.py,
which is a backport for Python 2 only. Given pypeFLOW does not
yet support Python 3 this is perhaps not worth noting, but I
marked this dependency as conditional.

* pypeFLOW 2 0 0 (#9065)

* Update for pypeFLOW v2.0.0

In the absense of an official tag on the upstream repository,
this is the commit which merged pull request 23 into the
master branch, and that included the version bump.

See PacificBiosciences/pypeFLOW#51

* Add basic about section to pypeFLOW recipe

* Fix URL for abundancebin (#9066)

* Remove duplicated pypeFLOW about metadata (#9068)

Keeps the license clarification, not just normal BSD.

* trigger; try out logic for divergent build strings

* Update: peddy, simple_sv_annotation, bcbio (#9069)

- peddy: latest development version with support for hg38. Drops
  bioconda patch which they incorporated upstream.
- simple_sv_annotation: Fix for REJECT filter not in VCF header.
- bcbio: support for moving output and better debugging with Cromwell.

* Revert "temporarly disable uploads for bulk branch"

This reverts commit 3cf5983.

* Update for pypeFLOW v2.0.1 (#9070)

In the absence of an official tag on the upstream repository,
this is the commit which merged pull request 26 into the
master branch, and that included the version bump.

See PacificBiosciences/pypeFLOW#51

* salmon v0.10.0

This bumps salmon to v0.10.0.  This release uses the `CONDA_BUILD=TRUE` flag during CMake configuration to force C++11 (instead of C++14) compilation.  Once conda-build 3 migration is complete, we should move this to build with C++14.

* AMPtk update to v1.2.3 (#9071)

* update to v1.2.3

* fix tab error

* Bissnp update (#9074)

* Updated to VERSION 1.0.1

* Fixed test.

* PacBio: Initial addition of `lima` (#9075)

* cyvcf2: remove plotting dependencies (see brentp/cyvcf2#83) (#9078)

* Update for pypeFLOW v2.0.2 (#9080)

In the absence of an official tag on the upstream repository,
this is the commit which merged pull request 33 into the
master branch, and that included the version bump.

See PacificBiosciences/pypeFLOW#51

* PacBio: Initial addition of `isoseq3` (#9076)

* rtg-tools: Update to 3.9.1 (#9077)

* PacBio: pull in lima as runtime dep for isoseq3 (#9081)

* This facilitates a simpler workflow, where all
  workflow dependencies are pulled in by just
  one recipe.

* Add rgbif and spocc recipes  (#9067)

* rgbif recipe created with conda skeleton cran

* fix recipes

* spocc recipe, build with conda skeleton cran

* enforce 2-space indentation

* enforce 2-space indentation

* first round of indentation fixes

* refactor

* recipes c-f whitespace

* recipes f-l whitespace

* recipes m-o whitespace

* recipes p-z whitespace

* migrate java recipes to noarch: generic (#9086)

* cleanup perl recipe

* fix all build/number sections and set it to 0

* fix all build/number sections and set it to 0

* change perl-threaded to perl

* fix recipes

* lint fixes again

* lint fixes

* lint fixes

* lint fixes

* lint fixes

* lint fixes

* lint fixes

* lint fixes

* lint fixes

* lint fixes

* lint fixes

* lint fixes

* remove fn: from all recipes

* fix linting

* lint fixes

* fix linting

* fix linting

* linting fix

* fix lint

* fix lint

* fix linting

* fix linting

* fix lint

* fix linting

* add more debug output to the lint step

* lint fixes

* lint fixes

* remove JE rc

* fix linting

* blacklist recipes found on conda-forge and defaults

* use --prelint for bioconda-utils build

* add script to bump builds

* fix merge

* fix merge

* bump build numbers for all recipes

* --prelint on bulk workflows

* add missing build numbers and set to 1

* adjustments for old viennnarna recipes

* bump build numbers.
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79 changes: 44 additions & 35 deletions .circleci/config.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,20 +2,27 @@ version: 2

variables:
restore_cache: &restore_cache
restore_cache:
keys:
- miniconda-{{ checksum ".circleci/common.sh" }}-{{ checksum ".circleci/setup.sh" }}-{{ checksum ".circleci/config.yml" }}-{{ arch }}
# TODO remove this temporal override before merging the PR into master
run: { command: echo 'ignoring cache' }
#restore_cache:
# keys:
# - miniconda-{{ checksum ".circleci/common.sh" }}-{{ checksum ".circleci/setup.sh" }}-{{ checksum ".circleci/config.yml" }}-{{ arch }}
save_cache: &save_cache
save_cache:
key: miniconda-{{ checksum ".circleci/common.sh" }}-{{ checksum ".circleci/setup.sh" }}-{{ checksum ".circleci/config.yml" }}-{{ arch }}
paths:
- miniconda
# TODO remove this temporal override before merging the PR into master
run: { command: echo 'ignoring cache' }
#save_cache:
# key: miniconda-{{ checksum ".circleci/common.sh" }}-{{ checksum ".circleci/setup.sh" }}-{{ checksum ".circleci/config.yml" }}-{{ arch }}
# paths:
# - miniconda
common: &common
run:
name: Download common definitions
command: curl -s https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh > .circleci/common.sh
command: |
curl -s https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh > .circleci/common.sh
# TODO remove this temporal override before merging the PR into master
echo -e 'MINICONDA_VER=4.4.10\nBIOCONDA_UTILS_TAG=cb3-migration' > .circleci/common.sh
setup: &setup
run:
run:
name: Setup bioconda-utils
command: .circleci/setup.sh
macos: &macos
Expand Down Expand Up @@ -56,7 +63,7 @@ jobs:
command: |
mkdir -p ~/.ssh
ssh-keyscan -H github.com >> ~/.ssh/known_hosts
- run:
- run:
name: Setup base system
command: |
cat >> $BASH_ENV <<EOF
Expand All @@ -70,11 +77,11 @@ jobs:
- *setup
- run:
name: Linting
command: bioconda-utils lint recipes config.yml --git-range master HEAD
command: bioconda-utils lint --loglevel debug --full-report recipes config.yml --git-range master HEAD
- run:
name: Testing
# Currently, using --docker below causes a permission error on Fedora 27,
# although it should be supported by the setup_remote_docker directive
# Currently, using --docker below causes a permission error on Fedora 27,
# although it should be supported by the setup_remote_docker directive
# above. A workaround or an upstream fix would be welcome.
command: bioconda-utils build recipes config.yml --git-range master HEAD

Expand All @@ -88,7 +95,7 @@ jobs:
- *save_cache
- run:
name: Linting
command: bioconda-utils lint recipes config.yml --git-range master HEAD
command: bioconda-utils lint --loglevel debug --full-report recipes config.yml --git-range master HEAD

# build and test on linux
test-linux:
Expand All @@ -101,7 +108,7 @@ jobs:
- *save_cache
- run:
name: Building and testing
command: bioconda-utils build recipes config.yml --git-range master HEAD --docker --mulled-test
command: bioconda-utils build recipes config.yml --git-range master HEAD --docker --mulled-test --prelint

# build and test on macos
test-macos:
Expand All @@ -114,8 +121,8 @@ jobs:
- *save_cache
- run:
name: Building and testing
command: bioconda-utils build recipes config.yml --git-range master HEAD
command: bioconda-utils build recipes config.yml --git-range master HEAD --prelint

# build, test and upload on linux
upload-linux:
<<: *linux
Expand All @@ -129,7 +136,7 @@ jobs:
# build only current commit (since we use squashed merging, this is safe)
- run:
name: Building, testing, and uploading
command: bioconda-utils build recipes config.yml --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers --git-range $CIRCLE_SHA1~1 $CIRCLE_SHA1
command: bioconda-utils build recipes config.yml --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers --git-range $CIRCLE_SHA1~1 $CIRCLE_SHA1 --prelint

# build, test and upload on macos
upload-macos:
Expand All @@ -144,7 +151,7 @@ jobs:
# build only current commit (since we use squashed merging, this is safe)
- run:
name: Building, testing and uploading
command: bioconda-utils build recipes config.yml --anaconda-upload --git-range $CIRCLE_SHA1~1 $CIRCLE_SHA1
command: bioconda-utils build recipes config.yml --anaconda-upload --git-range $CIRCLE_SHA1~1 $CIRCLE_SHA1 --prelint

# build, test and upload for bulk branch on linux
bulk-linux:
Expand All @@ -156,10 +163,9 @@ jobs:
- *restore_cache
- *setup
- *save_cache
# build everything that differs compared to master
- run:
name: Building, testing, and uploading of all unpublished recipes
command: bioconda-utils build recipes config.yml --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers --git-range master HEAD
command: bioconda-utils build recipes config.yml --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers --prelint

# build, test and upload for bulk branch on macos
bulk-macos:
Expand All @@ -171,11 +177,9 @@ jobs:
- *restore_cache
- *setup
- *save_cache
# build everything that differs compared to master
- run:
name: Building, testing and uploading of all unpublished recipes
command: bioconda-utils build recipes config.yml --anaconda-upload --git-range master HEAD

command: bioconda-utils build recipes config.yml --anaconda-upload --prelint

# nightly build, test and upload of unpublished recipes on linux
nightly-upload-linux:
Expand All @@ -189,7 +193,7 @@ jobs:
- *save_cache
- run:
name: Building, testing, and uploading of all unpublished recipes
command: bioconda-utils build recipes config.yml --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
command: bioconda-utils build recipes config.yml --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers --prelint

# nightly build, test and upload of unpublished recipes on macos
nightly-upload-macos:
Expand All @@ -203,7 +207,7 @@ jobs:
- *save_cache
- run:
name: Building, testing and uploading of all unpublished recipes
command: bioconda-utils build recipes config.yml --anaconda-upload
command: bioconda-utils build recipes config.yml --anaconda-upload --prelint



Expand All @@ -212,23 +216,28 @@ workflows:
# workflow for testing pushes and PRs
bioconda-test:
jobs:
- lint:
filters:
branches:
ignore:
- master
- bulk
# Linting is now performed just before a recipe is built with
# bioconda-utils build --prelint.
# TODO: remove this section if --prelint ends up working well.
# - lint:
# filters:
# branches:
# ignore:
# - master
# - bulk
- test-linux:
requires:
- lint
# TODO: remove if --prelint ends up working well
# requires:
# - lint
filters:
branches:
ignore:
- master
- bulk
- test-macos:
requires:
- lint
# TODO: remove if --prelint ends up working well
# - lint
- test-linux
filters:
branches:
Expand Down
6 changes: 3 additions & 3 deletions bootstrap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,9 @@

# This is the "common" step in the CircleCI config which gets the versions of
# Miniconda and bioconda-utils that we're using.
urlretrieve(
'https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh',
filename='.circleci/common.sh')
#urlretrieve(
# 'https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh',
# filename='.circleci/common.sh')


local_config_path = os.path.expanduser('~/.config/bioconda/activate')
Expand Down
80 changes: 80 additions & 0 deletions build-fail-blacklist
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Original file line number Diff line number Diff line change
Expand Up @@ -73,3 +73,83 @@ recipes/fermikit

# libxml2.so, not found
recipes/dcmtk


# The following recipes are also found in other channels (notably conda-forge).
# They are placed here on the blacklist until we can deal with them further.
recipes/aenum
recipes/intervaltree
recipes/jemalloc
recipes/jq
recipes/lapack
recipes/libdb
recipes/loompy
recipes/mysql-connector-c
recipes/nasm
recipes/netifaces
recipes/nglview
recipes/perl-text-soundex
recipes/popt
recipes/pysftp
recipes/pytest-timeout
recipes/python-levenshtein
recipes/r-argumentcheck
recipes/r-bio3d
recipes/r-biomark
recipes/r-cnogpro
recipes/r-data.table/1.10.4
recipes/r-deoptimr
recipes/r-diptest
recipes/r-diptest/0.75_7
recipes/r-drc
recipes/r-dynamictreecut
recipes/r-gam
recipes/r-gbm
recipes/r-genabel
recipes/r-genabel.data
recipes/r-genenet
recipes/r-giant
recipes/r-gprofiler
recipes/r-gpseq
recipes/r-grimport
recipes/r-gsalib
recipes/r-gsmoothr
recipes/r-haplo.stats
recipes/r-ic10trainingdata
recipes/r-icluster
recipes/r-idr
recipes/r-inlinedocs
recipes/r-km.ci
recipes/r-kmsurv
recipes/r-kriging
recipes/r-lsd
recipes/r-maldiquant
recipes/r-metarnaseq
recipes/r-microseq
recipes/r-mixomics
recipes/r-mlgt
recipes/r-mqtl
recipes/r-pamr
recipes/r-patpro
recipes/r-pinfsc50
recipes/r-plasmidprofiler
recipes/r-precrec
recipes/r-purbayes
recipes/r-qiimer
recipes/r-qtl
recipes/r-rcircos
recipes/r-readbrukerflexdata
recipes/r-readmzxmldata
recipes/r-rematch2
recipes/r-rentrez
recipes/r-robustrankaggreg
recipes/r-rphylip
recipes/r-seqinr
recipes/r-smvar
recipes/r-snpassoc
recipes/r-solarius
recipes/r-tfmpvalue
recipes/r-xnomial
recipes/regex
recipes/scikit-bio
recipes/xdg
9 changes: 3 additions & 6 deletions recipes/2pg_cartesian/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,22 +9,19 @@ package:

build:
skip: True #[osx]
number: 0
number: 1

source:
fn: v1.0.1.tar.gz
url: https://github.com/rodrigofaccioli/2pg_cartesian/archive/v1.0.1.tar.gz
md5: d97fcd5fff5cb0813d4ea918c57d991f

requirements:
build:
- gcc # [linux]
- llvm # [osx]
- {{ compiler('c') }}
- cmake
run:
- libgcc # [linux]
- gromacs

test:
commands:
- protpred-Gromacs-Test_random_number
- protpred-Gromacs-Test_random_number
34 changes: 16 additions & 18 deletions recipes/Migraine/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,30 +1,28 @@
package:
name: migraine
version: 0.5.2
name: migraine
version: 0.5.2

build:
number: 0
number: 1

source:
fn: migraine.tar.gz
url: http://kimura.univ-montp2.fr/%7Erousset/migraine05/migraine.tar.gz
sha256: ca2a20ee5b7b896de91cae2ec671785a1a2788d073bca4c0cf92cccb46060fbe
url: http://kimura.univ-montp2.fr/%7Erousset/migraine05/migraine.tar.gz
sha256: ca2a20ee5b7b896de91cae2ec671785a1a2788d073bca4c0cf92cccb46060fbe

requirements:
build:
- gcc
run:
- libgcc
build:
- {{ compiler('c') }}
run:

test:
commands:
- migraine | grep "Unable to open file migraine.txt"
commands:
- migraine | grep "Unable to open file migraine.txt"

about:
home: http://kimura.univ-montp2.fr/~rousset/Migraine.htm
license: CeCILL
summary: Implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently  handled are allelic counts but sequences will be handled in the forthcoming version.
home: http://kimura.univ-montp2.fr/~rousset/Migraine.htm
license: CeCILL
summary: Implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently  handled are allelic counts but sequences will be handled in the forthcoming version.
extra:
identifiers:
- biotools:Migraine
- doi:10.1093/molbev/msu212
identifiers:
- biotools:Migraine
- doi:10.1093/molbev/msu212
2 changes: 1 addition & 1 deletion recipes/SpliceMap/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ package:
version: 3.3.5.2

build:
number: 0
number: 1

source:
fn: SpliceMap3352_linux-64.zip
Expand Down
3 changes: 1 addition & 2 deletions recipes/a5-miseq/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,11 @@ package:
version: {{ version }}

source:
fn: {{ name|lower }}-{{ version }}.tar.gz
url: https://sourceforge.net/projects/ngopt/files/a5_miseq_linux_20160825.tar.gz/
sha256: 76a2798d617d45f4539e73ef2df5f899503ac4a54c3a406faf37db6282127fe9

build:
skip: True # [osx]
skip: True # [osx]
number: {{ build }}

requirements:
Expand Down
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