[BULK] Bioconductor 3.8#12545

Merged

bgruening merged 531 commits intobulkfrom bioc3.8_071218

Dec 9, 2018

+169,545-14,159

This pull request is big! We're only showing the most recent 250 commits

Commits on Nov 17, 2018

Fix octopus binary "invalid instruction" (-march too new) (#11822 )

holtgrewe
authored and
epruesse
committed
Update perl-bio-asn1-entrezgene to 1.73 (#11914 )
epruesse
authored
Update perl-file-slurp to 9999.25 (#12127 )

epruesse
authored and
druvus
committed
Update manta to 1.5.0 (#12126 )

epruesse
authored and
druvus
committed
Update nanocomp to 1.0.0 (#12124 )

epruesse
authored and
druvus
committed
Update masurca to 3.2.9 (#12121 )

epruesse
authored and
druvus
committed
Update beagle-lib to 3.1.1 (#12119 )
epruesse
authored
Update r-spocc to 0.9.0 (#12118 )
epruesse
authored
Update kallisto to 0.45.0 (#12117 )
epruesse
authored
Update validators to 0.12.3 (#12116 )
epruesse
authored
Update illumina-interop to 1.1.7 (#12115 )
epruesse
authored
Update umi_tools to 0.5.5 (#12123 )
epruesse
authored
Update tiptoft to 1.0.0 (#12122 )
epruesse
authored
Update: TitanCNA with fix for hg38 plotting (#12130 )
chapmanb
authored
blockclust (#12111 )

pavanvidem
authored and
bgruening
committed

Commits on Nov 19, 2018

Commits on Nov 22, 2018

Findbin::Real added (#12291 )
jfallmann
authored
Added version bump to 1.3 (#12292 )
apeltzer
authored
ngs-bits 2018_11 (#12262 )

marc-sturm
authored and
apeltzer
committed
minor edit in grid (#12287 )
aemiol
authored
Fred2 update (#12259 )
apeltzer
authored
msstitch version 2.9 (#12296 )
glormph
authored
r-mvr (#12300 )
Chris-Lowe-Integrity
authored
Bump to Gromacs 2018.3 + re-enable OSX build (#12299 )
stain
authored
pyGenomeTracks update of dependencies (#12279 )
joachimwolff
authored
Gromacs 2018.4 (#12302 )
stain
authored
quast 5.0.2 (#12303 )

alexeigurevich
authored and
stain
committed
Update meta.yaml (#12275 )

richjstark
authored and
stain
committed
Use the extended-base container because of wget issues when downloading databases (#12297 )

pvanheus
authored and
stain
committed
Update duphold to 0.1.0 (#12257 )

epruesse
authored and
stain
committed
Update flashlfq to 0.1.109 (#12256 )

epruesse
authored and
stain
committed
Update planemo to 0.57.0 (#12251 )

epruesse
authored and
stain
committed
Update meta.yaml (#12258 )

TomSmithCGAT
authored and
stain
committed
Update scalpel to 0.5.4 (#12249 )

epruesse
authored and
stain
committed
edit grid (#12298 )
aemiol
authored
added feather to deps (#12293 )

simonvh
authored and
bgruening
committed
R tigger (#12286 )
PertuyF
authored

Commits on Nov 23, 2018

Commits on Nov 24, 2018

Added nimnexus [v0.1] (#12133 )
Avsecz
authored
[WIP] Add R-loom (#12320 )

mtekman
authored and
bgruening
committed
Create Changeo recipe (#12321 )
PertuyF
authored
r-corbi (#12325 )
Christopher Lowe
authored

Commits on Nov 25, 2018

r-nam (#12327 )
Christopher Lowe
authored
Update pybedtools to 0.8.0 (#12324 )
daler
authored
MSGFplus does not work with newer Java (#12330 )

glormph
authored and
bgruening
committed
Update atropos to 1.1.21 (#12322 )

jdidion
authored and
bgruening
committed
Update CONCOCT to 0.4.2 (#12317 )

alneberg
authored and
bgruening
committed

Commits on Nov 26, 2018

New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331 )
chapmanb
authored
Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332 )

glormph
authored and
bgruening
committed
Update Picard to 2.18.17. (#12333 )
cbrueffer
authored
Unblacklist IgDiscover (#12335 )
marcelm
authored
PacBio: Add missing licenses and post-link message (#12334 )

pb-dseifert
authored and
SoapZA
committed
Bioconductor DEqMS package (#12336 )

glormph
authored and
bgruening
committed
Genenotebook v0.1.10 (#12337 )
holmrenser
authored
removed cloudpickle requirement for blockclust (#12242 )

pavanvidem
authored and
bgruening
committed
R guilds (#12341 )
Christopher Lowe
authored
Strict rec (#12113 )
ursky
authored
Update qcat to v1.0.1 (#12343 )
philres
authored

Commits on Nov 27, 2018

Add better error checking (#12345 )
pvanheus
authored
Add mhcnames python package (#12349 )
Leon Kuchenbecker
authored
Add MHCflurry pMHC class I binding affinity prediction tool (#12346 )
Leon Kuchenbecker
authored
Bump pilon (#12354 )
druvus
authored
Update pronto to 0.11.1 (#12377 )

epruesse
authored and
bgruening
committed
Update perl-json-xs to 4.0 (#12373 )

epruesse
authored and
bgruening
committed
Update planemo to 0.57.1 (#12370 )

epruesse
authored and
bgruening
committed
Update snippy to 4.3.6 (#12372 )

epruesse
authored and
bgruening
committed
Update intarna to 2.3.1 (#12367 )

epruesse
authored and
bgruening
committed
Update agfusion to 1.231 (#12366 )

epruesse
authored and
bgruening
committed
Update bioconda-utils to 0.15.0 (#12359 )

epruesse
authored and
bgruening
committed
Update mapdamage2 to 2.0.9 (#12358 )

epruesse
authored and
bgruening
committed
Update scanpy to 1.3.4 (#12357 )

epruesse
authored and
bgruening
committed
Update goatools to 0.8.11 (#12361 )

epruesse
authored and
bgruening
committed
Update perl-math-random-mt-auto to 6.23 (#12362 )

epruesse
authored and
bgruening
committed
Update kipoi to 0.6.3 (#12374 )
epruesse
authored
Update kipoi_veff to 0.2.1 (#12364 )

epruesse
authored and
Avsecz
committed
Update perl-object-insideout to 4.05 (#12380 )
epruesse
authored
Update sevenbridges-python to 0.17.1 (#12379 )
epruesse
authored
Update nanosv to 1.2.3 (#12378 )
epruesse
authored
Update starfish to 0.0.30 (#12368 )
epruesse
authored
Update clust to 1.8.10 (#12356 )
epruesse
authored
Update pypairs to 2.0.6 (#12381 )
epruesse
authored
Update khmer to 3.0.0a2 (#12360 )
epruesse
authored

Commits on Nov 28, 2018

Update flashlfq to 0.1.110 (#12385 )
epruesse
authored
Update perl-algorithm-cluster to 1.57 (#12384 )
epruesse
authored
Update arvados-python-client to 1.2.0.20181121194423 (#12382 )
epruesse
authored
Update avro-cwl to 1.8.9 (#12355 )
epruesse
authored
r-breakaway (#12386 )
Christopher Lowe
authored
R sads (#12388 )
Christopher Lowe
authored
Update python-sortedcontainers to 2.1.0 (#12383 )
epruesse
authored
r-ebimetagenomics (#12339 )
Christopher Lowe
authored
pin armadilo on major version (#12389 )
epruesse
authored
IgDiscover version 0.11 (#12351 )
marcelm
authored
Update goatools to 0.8.12 (#12391 )
epruesse
authored
Update bioconda-utils to 0.15.1 (#12390 )
epruesse
authored
R ebimetagenomics (#12393 )
Christopher Lowe
authored
Add dimspy recipes for reference purposes (#12387 )

RJMW
authored and
bgruening
committed
Added BioExcel_SeqQC to bioconda-recipes (#12276 )

djwhiteastro
authored and
bgruening
committed
PacBio: Update pbalign to 0.3.2 (#12396 )
pb-dseifert
authored
add bgreat to bioconda (#12350 )

Malfoy
authored and
natir
committed
btrim integration to conda (#12395 )

Malfoy
authored and
natir
committed
Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399 )
johanneskoester
authored
PacBio: Update pbsv2 to version 2.1.0 (#12400 )
armintoepfer
authored
Genenotebook v0.1.11 (#12398 )
holmrenser
authored
prosolo: new package version 0.6.0 (#12397 )

dlaehnemann
authored and
epruesse
committed
Update sevenbridges-python to 0.17.2 (#12404 )
epruesse
authored
Add recipe for ICED (#12406 )
npavlovikj
authored

Commits on Nov 29, 2018

Downgrade version for iced (#12409 )
npavlovikj
authored
Update recipe for libstatgen 1.0.5 (#12348 )
npavlovikj
authored
Update iced to 0.5.0 (#12411 )
epruesse
authored
Update perl-test2-suite to 0.000116 (#12412 )
epruesse
authored
fix compatibility with other tools (#12415 )

Malfoy
authored and
natir
committed
Restore dexseq python helper scripts (#12352 )
lparsons
authored
Genenotebook v0.1.12 (#12418 )
holmrenser
authored
added medpy recipe (#12417 )
ThomasWollmann
authored
Updated ddrage to version 1.6.1. (#12421 )
HenningTimm
authored
Add r-mcpcounter recipe. (#12261 )

grst
authored and
epruesse
committed
Update DEXSeq requirements to force compatible HTSeq version (#12423 )
lparsons
authored
ARB: Pin glib (#11782 )
epruesse
authored
Update meta.yaml (#12426 )

bgruening
authored and
epruesse
committed
stacks: fix for fix 'fixing' @ in exe_path (#12420 )

bernt-matthias
authored and
epruesse
committed
Genenotebook v0.1.13 (#12424 )

holmrenser
authored and
epruesse
committed

Commits on Nov 30, 2018

metaQuantome (#12413 )
Caleb Easterly
authored
New MMseqs2 release 7-4e23d (#12432 )
martin-steinegger
authored
update spades to 3.13.0 (#12408 )
notestaff
authored
Update Crossmap to 0.3.1 (#12439 )
vladsavelyev
authored
Make metaquantome dependencies more specific (#12442 )
Caleb Easterly
authored
integration of bcool to bioconda (#12422 )

Malfoy
authored and
natir
committed
Update hifive to 1.5.7 (#12433 )

epruesse
authored and
bgruening
committed
Update scvi to 0.2.3 (#12434 )

epruesse
authored and
bgruening
committed
Update Subread from 1.6.2 to 1.6.3. (#12425 )

jdblischak
authored and
bgruening
committed
UCSC Cell Browser 0.4.23 (#12347 )
pcm32
authored
Update libstatgen to 1.0.14 (#12437 )
epruesse
authored
Update arvados-python-client to 1.2.1 (#12438 )
epruesse
authored
Update tirmite to 1.1.3 (#12435 )
epruesse
authored
Bump metaquantome (#12449 )
Caleb Easterly
authored
Update ADAM to 0.25.0 (#12445 )

heuermh
authored and
epruesse
committed

Commits on Dec 3, 2018

Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453 )
chapmanb
authored
update rgi4.2.2 recipe (#12282 )

mjram0s
authored and
apetkau
committed
Add CRAN R package leapp. (#12428 )

jdblischak
authored and
souravsingh
committed
Bump DECIPHER to Bioconductor 3.7 (#12463 )

apcamargo
authored and
souravsingh
committed
updated scVI to 0.2.3 (#12429 )

romain-lopez
authored and
souravsingh
committed
Add recipe for PyAAVF 0.1.0 (#12451 )

camytran
authored and
souravsingh
committed
seqkit 0.9.3 (#12455 )

shenwei356
authored and
souravsingh
committed
HTSeq - Pin numpy version (#12467 )

lparsons
authored and
epruesse
committed
update eigensoft to 7.2.1 (#12469 )
ryanraaum
authored
Update scnic to 0.6.0 (#12436 )
epruesse
authored

Commits on Dec 5, 2018

Adding recipe for clinvar-tsv v0.1.0. (#12481 )
holtgrewe
authored
no fixed boost version (#12483 )
tobiasrausch
authored
New recipe: pysradb (#12470 )

saketkc
authored and
druvus
committed
Pyseer 1.2.0 (#12444 )

mgalardini
authored and
druvus
committed
sentieon: minor version bump to 201808.01 (#12480 )

Lenbok
authored and
chapmanb
committed
adding java to mutations recipe (#12485 )
asmariyaz23
authored
Update ncrf to 1.00.06 (#12369 )

epruesse
authored and
druvus
committed
Bump umitools (#12486 )
druvus
authored
Mob suite version 1.4.9 no arch build number 2 (#12479 )

kbessonov1984
authored and
druvus
committed
Update r-goeveg to 0.4.2 (#12375 )

epruesse
authored and
druvus
committed
Removes r-seurat-scripts from blacklisting (#12489 )

pcm32
authored and
pinin4fjords
committed
For VarDict-Java, install utility scripts. (#12488 )

cbrueffer
authored and
chapmanb
committed
Pin compatible numpy for older HTSEQ versions (#12490 )

lparsons
authored and
bgruening
committed
add recipe for r-epic (#12473 )

grst
authored and
souravsingh
committed
Add new recipe - RVTESTS (#12465 )

zhanxw
authored and
souravsingh
committed
Adding recipe for var-agg v0.1.0 (#12482 )
holtgrewe
authored
Adding var-agg v0.1.1. (#12495 )
holtgrewe
authored

Commits on Dec 7, 2018