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Bulk #18029

Merged
merged 334 commits into from
Oct 11, 2019
Merged

Bulk #18029

merged 334 commits into from
Oct 11, 2019

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dpryan79
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Bioconda requires reviews prior to merging pull-requests (PRs). To facilitate this, once your PR is passing tests and ready to be merged, please add the please review & merge label so other members of the bioconda community can have a look at your PR and either make suggestions or merge it. Note that if you are not already a member of the bioconda project (meaning that you can't add this label), please ping @bioconda/core so that your PR can be reviewed and merged (please note if you'd like to be added to the bioconda project). Please see #15332 for more details.

  • 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).

bgruening and others added 30 commits December 29, 2018 16:34
* more updates

* update mageckflute
* bulk updates

* a couple more updates
* Bulk updates for 040119

* update blacklist

* update champ
* a few updates

* Remove bld.bat
* updates

* Update build.sh

* Update build.sh
* update camera, cosmiq, and metab

* update blacklist
dpryan79 and others added 28 commits August 18, 2019 12:04
* Update sourmash to 2.1.0 (#17113)

* Update aquila_stlfr to 1.2.9 (#17111)

* Update pynnotator to add support for Python2 (#17114)

* Update pynnotator to add support for Python2

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update sevenbridges-python to 0.23.1 (#17117)

* Update pbmm2 to 1.1.0 (#17072)

* Update pbmm2 to 1.1.0
* PacBio: Update `pbmm2` dependencies

* Update nanoplot to 1.27.0 (#17118)

* Update nanoget to 1.9.0 (#17116)

* Update cgpbigwig to 1.0.4 (#16970)

* Update cgpbigwig to 1.0.4

* Update cgpbigwig to 1.0.4

* Works on linux

* just wondering...

* p11-kit is linux only

* Update varfish-annotator-cli to 0.10 (#17121)

* Update flashlfq to 1.0.0 (#17123)

* pb-falconc-0.0.1 (#17077)

* pb-falconc-0.0.1

* Try to find missing gcc

* Try another way

CircleCI does not find "gcc", so I will try a newer way.

* We are looking for gcc.

Maybe this will help us find it.

* Closer

```
01:16:51 BIOCONDA INFO (OUT) echo "CC=$CC"
CC=/opt/conda/conda-bld/pb-falconc_1566695732043/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
CC=$BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc
```

* alias gcc maybe?

* Try symlinking gcc

* further nim compilation

* get nim to build

* apparently this needs rsync to copy some directories.

* try injecting compilers

* should compile on Linux at least

* better compiler injection

* Update clonalframeml to 1.12 (#17120)

* Update clonalframeml to 1.12

* C++, inject compilers

* Adding jupyterpngsplugin python package to Bioconda (#17124)

* SEPP: Update to version 4.3.10 (#16958)

* Update to version 4.3.10

fix issue #70 a bug when hmmsearch fake jobs where not piped

* search binaries in $PREFIX

instead of relying on conda's preprocessing and replacing of /opt/anaconda1anaconda2anaconda3/

* debugging

* debug a bit, this actually passes locally, possibly due to a different conda-build version

* Update meta.yaml

* more debugging

* maybe

* no slash?

* not in . directories

* remove debug test

* Update aquila_stlfr to 1.2.10 (#17125)

* Update r-bioverbs to 0.2.7 (#17127)

* Update r-goalie to 0.3.6 (#17130)

* Update r-syntactic to 0.2.4 (#17132)

* Update angsd to 0.931 (#14862)

* Update angsd to 0.929

* Update angsd to 0.931

* start simplifying

* foo

* tidy up

* Update womtool to 45.1 (#17126)

* bump platon mummer dependency version (3->4) (#17119)

* Update r-transformer to 0.2.5 (#17135)

* Update neurodocker to 0.5.0. (#17137)

* clean and build, fail on errors, issue #11509 (#17085)

* clean and build, fail on errors, issue #11509

* fix linting

* This builds on linux

* Update meta.yaml

* Adding goenrichment python package (#17131)

* Adding goenrichment python package

* Update meta.yaml

* bump iranges to 2.18.2 (#17138)

* bump iranges to 2.18.2

* Update r-transformer

* Update r-brio to 0.3.6 (#17134)

* Update r-freerange to 0.2.4 (#17133)

* Update r-freerange to 0.2.4

* Update meta.yaml

* typo

* Update r-basejump to 0.11.11 (#17136)

* Update r-basejump to 0.11.11

* update dependencies

* snakemake: require imagemagick >= 7.0 to avoid PDF -> PNG convert bug (#17062)

* Update sevenbridges-python to 0.23.2 (#17139)


Package uploads complete: [ci skip]
 - biocontainers/sevenbridges-python:0.23.2--py_0
 - noarch/sevenbridges-python-0.23.2-py_0.tar.bz2

* Smudgeplot (#17140)

* First attempt at recipe

* Added R package dependencies

* Added numpy dependency

* Added scipy

* Fixed test

* Testing suggestions from PR

* Final polishing after PR comments - passed local tests

* Get the R stuff in the right place to ensure the pinning works

* Update gridss to 2.5.2 (#17143)

* Remove minepy for conda-forge/staged-recipes#9292 (#17146)

* aquila first version (#17129)

* first version

* modify meta for bioconda install

* Update meta.yaml

* Update pynnotator to 1.9 (#17145)

* Update pynnotator to 1.9

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update plasmidfinder to 2.1 (#17147)


Package uploads complete: [ci skip]
 - biocontainers/plasmidfinder:2.1--0
 - noarch/plasmidfinder-2.1-0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@gmail.com>

* Include target dir for clean as well to ensure right location is cleane

* Include target dir for clean as well to ensure right location is cleaned

* bump build number

* Update downpore to 0.3.3 (#12573)


Package uploads complete: [ci skip]
 - biocontainers/downpore:0.3.3--h375a9b1_0
 - linux-64/downpore-0.3.3-h375a9b1_0.tar.bz2
 - osx-64/downpore-0.3.3-h375a9b1_0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@gmail.com>

* Update gprofiler-official to 1.0.0 (#12213)


Package uploads complete: [ci skip]
 - biocontainers/gprofiler-official:1.0.0--py_0
 - noarch/gprofiler-official-1.0.0-py_0.tar.bz2

Co-authored-by: BiocondaBot <47040946+biocondabot@users.noreply.github.com>
Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
Co-authored-by: Devon Ryan <dpryan79@gmail.com>

* Update rust-bio-tools to 0.6.0 (#17149)


Package uploads complete: [ci skip]
 - biocontainers/rust-bio-tools:0.6.0--hf53bd2b_0
 - linux-64/rust-bio-tools-0.6.0-hf53bd2b_0.tar.bz2
 - osx-64/rust-bio-tools-0.6.0-h9904429_0.tar.bz2

* fix and update r-spieceasi (#17148)


Package uploads complete: [ci skip]
 - biocontainers/r-spieceasi:1.0.7--r36_0
 - noarch/r-spieceasi-1.0.7-r36_0.tar.bz2

Co-authored-by: Zachary Kurtz <zkurtz@lodotherapeutics.com>

* Update control-freec to 11.5 (#12199)


Package uploads complete: [ci skip]
 - biocontainers/control-freec:11.5--he1b5a44_0
 - linux-64/control-freec-11.5-he1b5a44_0.tar.bz2
 - osx-64/control-freec-11.5-h6de7cb9_0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@gmail.com>

* minced 0.4.0 - build with older java (#17150)

* Update epic2 to 0.0.40 (#17152)


Package uploads complete: [ci skip]
 - biocontainers/epic2:0.0.40--py27h9276139_0
 - biocontainers/epic2:0.0.40--py36h9276139_0
 - biocontainers/epic2:0.0.40--py37h9276139_0
 - linux-64/epic2-0.0.40-py27h9276139_0.tar.bz2
 - linux-64/epic2-0.0.40-py36h9276139_0.tar.bz2
 - linux-64/epic2-0.0.40-py37h9276139_0.tar.bz2

* Update scanpy-scripts to 0.2.4.post1 (#17151)


Package uploads complete: [ci skip]
 - biocontainers/scanpy-scripts:0.2.4.post1--py_0
 - noarch/scanpy-scripts-0.2.4.post1-py_0.tar.bz2

Co-authored-by: BiocondaBot <47040946+biocondabot@users.noreply.github.com>

* Update howdesbt to 1.00.03 (#16920)


Package uploads complete: [ci skip]
 - biocontainers/howdesbt:1.00.03--hc9558a2_0
 - linux-64/howdesbt-1.00.03-hc9558a2_0.tar.bz2
 - osx-64/howdesbt-1.00.03-h770b8ee_0.tar.bz2

Co-authored-by: dpryan79 <dpryan79@gmail.com>
Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>

* Update pynnotator to 1.9.1 (#17154)


Package uploads complete: [ci skip]
 - biocontainers/pynnotator:1.9.1--py_0
 - noarch/pynnotator-1.9.1-py_0.tar.bz2

* Update paragraph to 2.3 (#16539)


Package uploads complete: [ci skip]
 - biocontainers/paragraph:2.3--h8908b6f_0
 - linux-64/paragraph-2.3-h8908b6f_0.tar.bz2

Co-authored-by: dpryan79 <dpryan79@gmail.com>
Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>

* Update hmmratac to 1.2.7 (#17158)


Package uploads complete: [ci skip]
 - biocontainers/hmmratac:1.2.7--0
 - noarch/hmmratac-1.2.7-0.tar.bz2

* Update libdeflate to 1.3 (#16839)

* Update libdeflate to 1.3

* libdeflate has been migrated to conda-forge

* Updated RNAlien to version 1.7.0 (#17153)

* Updated RNAlien to version 1.7.0

* Removed echo and merged mv to one line

guess the echo is for debugging and moving directly to ${t}-bin gets rid of a mv operation

* Updated checksum

* Fixed path

* Added debug output

* Fix for path

* creating bin dir

* creating bin dir in prefix

* Minor

Remove ls commands as they are debug only, added -p option to mkdir to prevent fail and only create dir if not existing

* Update rnasamba to 0.1.4 (#17164)

* Fix cromshell dependency (#17160)


Package uploads complete: [ci skip]
 - biocontainers/cromshell:0.3.10--1
 - noarch/cromshell-0.3.10-1.tar.bz2

* Update rnasamba to 0.1.4 (#17168)


Package uploads complete: [ci skip]
 - biocontainers/rnasamba:0.1.4--py_0
 - noarch/rnasamba-0.1.4-py_0.tar.bz2

* Update dca to 0.2.3 (#17165)


Package uploads complete: [ci skip]
 - biocontainers/dca:0.2.3--py_0
 - noarch/dca-0.2.3-py_0.tar.bz2

* Bump build number. (#17159)


Package uploads complete: [ci skip]
 - biocontainers/pysamstats:1.1.2--py27hed695b0_5
 - biocontainers/pysamstats:1.1.2--py36hed695b0_5
 - biocontainers/pysamstats:1.1.2--py37hed695b0_5
 - linux-64/pysamstats-1.1.2-py27hed695b0_5.tar.bz2
 - linux-64/pysamstats-1.1.2-py36hed695b0_5.tar.bz2
 - linux-64/pysamstats-1.1.2-py37hed695b0_5.tar.bz2
 - osx-64/pysamstats-1.1.2-py27h2573ce8_5.tar.bz2
 - osx-64/pysamstats-1.1.2-py36h2573ce8_5.tar.bz2
 - osx-64/pysamstats-1.1.2-py37h2573ce8_5.tar.bz2

* Updating homer to version 4.10 and removing it from the blacklist (#17162)


Package uploads complete: [ci skip]
 - biocontainers/homer:4.10--pl526hc9558a2_0
 - linux-64/homer-4.10-pl526hc9558a2_0.tar.bz2
 - osx-64/homer-4.10-pl526h770b8ee_0.tar.bz2

* Update masurca to 3.3.3 (#15706)


Package uploads complete: [ci skip]
 - biocontainers/masurca:3.3.3--pl526haae6466_0
 - linux-64/masurca-3.3.3-pl526haae6466_0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@gmail.com>

* Update presto to 0.5.13 (#17167)


Package uploads complete: [ci skip]
 - biocontainers/presto:0.5.13--py_0
 - noarch/presto-0.5.13-py_0.tar.bz2

* Update cat to 5.0 (#17163)


Package uploads complete: [ci skip]
 - biocontainers/cat:5.0--0
 - noarch/cat-5.0-0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>

* Update askocli to 0.5 (#15847)


Package uploads complete: [ci skip]
 - biocontainers/askocli:0.5--py_0
 - noarch/askocli-0.5-py_0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>

* Recipe for MotifBinner2 version 2.0.0 (#17141)


Package uploads complete: [ci skip]
 - biocontainers/r-motifbinner:2.0.0--r36he1b5a44_0
 - linux-64/r-motifbinner-2.0.0-r36he1b5a44_0.tar.bz2
 - osx-64/r-motifbinner-2.0.0-r36h6de7cb9_0.tar.bz2

* Update breseq to 0.33.2 (#12188)


Package uploads complete: [ci skip]
 - biocontainers/breseq:0.33.2--h8b12597_0
 - linux-64/breseq-0.33.2-h8b12597_0.tar.bz2
 - osx-64/breseq-0.33.2-hfbae3c0_0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@gmail.com>

* Update spine to 0.3.2 (#12175)


Package uploads complete: [ci skip]
 - biocontainers/spine:0.3.2--pl526_0
 - noarch/spine-0.3.2-pl526_0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
Co-authored-by: Devon Ryan <dpryan79@gmail.com>

* Update cwltest to 1.0.20190228134645 (#15889)


Package uploads complete: [ci skip]
 - biocontainers/cwltest:1.0.20190228134645--py_0
 - noarch/cwltest-1.0.20190228134645-py_0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@gmail.com>

* Update star to 2.7.2b (#17169)

* pbbam: revdep rebuilds (#17161)

* Update rename to 1.601 (#17170)


Package uploads complete: [ci skip]
 - biocontainers/rename:1.601--0
 - noarch/rename-1.601-0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>

* Update minced to 0.4.1 (#17171)


Package uploads complete: [ci skip]
 - biocontainers/minced:0.4.1--0
 - noarch/minced-0.4.1-0.tar.bz2

Co-authored-by: dpryan79 <dpryan79@gmail.com>

* Update netreg to 1.8.0 (#16936)


Package uploads complete: [ci skip]
 - biocontainers/netreg:1.8.0--h9fd3d4c_0
 - linux-64/netreg-1.8.0-h9fd3d4c_0.tar.bz2
 - osx-64/netreg-1.8.0-hf0ff744_0.tar.bz2

Co-authored-by: dpryan79 <dpryan79@gmail.com>

* Update tadtool to 0.79 (#17173)


Package uploads complete: [ci skip]
 - biocontainers/tadtool:0.79--py_0
 - noarch/tadtool-0.79-py_0.tar.bz2

* pbbam: revdep rebuilds #2 (#17174)


Package uploads complete: [ci skip]
 - biocontainers/bax2bam:0.0.9--h018d624_7
 - biocontainers/blasr:5.3.3--h018d624_1
 - linux-64/bax2bam-0.0.9-h018d624_7.tar.bz2
 - linux-64/blasr-5.3.3-h018d624_1.tar.bz2
 - osx-64/bax2bam-0.0.9-h13b73d5_7.tar.bz2
 - osx-64/blasr-5.3.3-h13b73d5_1.tar.bz2

* Update r-exomedepth to 1.1.12 (#17175)

* Update r-exomedepth to 1.1.12

* Update meta.yaml

* Update mutmap to 2.1.0 (#17176)


Package uploads complete: [ci skip]
 - biocontainers/mutmap:2.1.0--py_0
 - noarch/mutmap-2.1.0-py_0.tar.bz2

* Update qtlseq to 2.0.3 (#17177)


Package uploads complete: [ci skip]
 - biocontainers/qtlseq:2.0.3--py_0
 - noarch/qtlseq-2.0.3-py_0.tar.bz2

* Update pyranges to 0.0.52 (#17178)


Package uploads complete: [ci skip]
 - biocontainers/pyranges:0.0.52--py36h516909a_0
 - biocontainers/pyranges:0.0.52--py37h516909a_0
 - linux-64/pyranges-0.0.52-py36h516909a_0.tar.bz2
 - linux-64/pyranges-0.0.52-py37h516909a_0.tar.bz2
 - osx-64/pyranges-0.0.52-py36h01d97ff_0.tar.bz2
 - osx-64/pyranges-0.0.52-py37h01d97ff_0.tar.bz2

* simka-1.5.0 (#16670)

* simka-1.5.0

* Update mobidic-mpa to 1.1.2 (#17181)


Package uploads complete: [ci skip]
 - biocontainers/mobidic-mpa:1.1.2--py_0
 - noarch/mobidic-mpa-1.1.2-py_0.tar.bz2

* Update popdel to 1.1.2 (#17182)


Package uploads complete: [ci skip]
 - biocontainers/popdel:1.1.2--he513fc3_0
 - linux-64/popdel-1.1.2-he513fc3_0.tar.bz2
 - osx-64/popdel-1.1.2-h2dec4b4_0.tar.bz2

* Create variable (this has been removed in 7624ae9 by mistake).

* Set shell options.

* Set shebang and shell options.

* Use a HEREDOC for ${PREFIX}/.message.txt.

* Bump build number.

* Remove blank line.

* I wonder

* guess that didn't work
@dpryan79
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I'll use my admin rights to merge this later tonight.

@dpryan79 dpryan79 merged commit c7adbb6 into master Oct 11, 2019
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3 participants