Bulk #18260
Merged
Bulk #18260
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* more updates * update mageckflute
* bulk updates * a couple more updates
* Bulk updates for 040119 * update blacklist * update champ
* a few updates * Remove bld.bat
* update camera, cosmiq, and metab * update blacklist
* 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 * bioconductor-rnaseqpower * more blacklisted packages * A few last updates
* A few more updates * Fix python in dexseq, since the count script has system requirements that aren't listed
* 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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 & mergelabel 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/coreso 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.