Bulk #18029
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Bulk #18029
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* 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
…d of hardcoded value.
…e files of this recipe are copied).
* 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
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I'll use my admin rights to merge this later tonight. |
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