STAR-Fusion crashes because of missing DB_File module #3
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Fixed. DB_File can be build separately. |
mbargull
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Jan 30, 2018
Update from upstream repo bioconda/bioconda-recipes
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Feb 12, 2019
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mbargull
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Jul 16, 2019
dpryan79
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Aug 16, 2019
* First attempt at a recipe for PhyloCSF * Reset build number to 0; Added basic test; Added license (CLI round 1 errors) * Lowercased package name (CLI round 2) * changed folder name to match package name (CLI round 3) * Added manual download and compiling of Opam * Added wget as requirement * Added opam setup step * Attempt to fix opam install process: added unzip and glpk dependencies, build without sandboxing * test with g++ instead of gcc * Fix attempt for missing solver * Second attempt at c++ compiler * Added messages for better debugging * Attempt to change opam install mode to binaries * It works locally now ... * Forgot to revert curl to wget ... * Added -y option to opam install * Fix attempt for OCaml package compiling bugs * Second fix attempt for OCaml package compiling bugs * Debugging gsl-conf + see if I can remove some dependencies * Debugging gsl-conf #2 * Debugging gsl-conf #3 * Debugging gsl-conf #4 * Debugging gsl-conf #5 * Debugging gsl-conf #5 * Debugging gsl-conf #6 * Cleaned up, small test * Checking output from pkg-config gsl * Checking output from pkg-config gsl - 2 * Checking output from pkg-config gsl - 3 * Test with pkg-config * Testing pkgconfig path + removed exporting ld path * More pkg-config testing * More pkg-config testing * More pkg-config testing * More pkg-config testing * Testing after candidate fixs * Cleaned up recipe after successful tests for GSL, added ocamlfind package to opam * Updated PhyloCSF archive to new release that fixes makefile for new compilers * Cleanup, candidate for final recipe 1 * Added gsl to runtime to fix missing gsl shared library in tests * Removed the accidental 0 that I added at the end of build.sh ... * Added test files to source_files in metal.yaml test section * Manually moved file required for test in bin, less clean but otherwise mulled-build fails as test file is missing * woops * Fix attempt for test file * Removed test as it required a file and failed in mulled-build since the file was not present * I don't know why tests are failing * Removed test at the moment * First attempt at implementing tests properly * Second attempt at implementing tests properly * Updated test * Trying to understand testing environment * Test with * Test with 2 * Test with PREFIX 3 * Tentative fix to build on OSX * First attempt at a recipe for PhyloCSF * Reset build number to 0; Added basic test; Added license (CLI round 1 errors) * Lowercased package name (CLI round 2) * changed folder name to match package name (CLI round 3) * Added manual download and compiling of Opam * Added wget as requirement * Added opam setup step * Attempt to fix opam install process: added unzip and glpk dependencies, build without sandboxing * test with g++ instead of gcc * Fix attempt for missing solver * Second attempt at c++ compiler * Added messages for better debugging * Attempt to change opam install mode to binaries * It works locally now ... * Forgot to revert curl to wget ... * Added -y option to opam install * Fix attempt for OCaml package compiling bugs * Second fix attempt for OCaml package compiling bugs * Debugging gsl-conf + see if I can remove some dependencies * Debugging gsl-conf #2 * Debugging gsl-conf #3 * Debugging gsl-conf #4 * Debugging gsl-conf #5 * Debugging gsl-conf #5 * Debugging gsl-conf #6 * Cleaned up, small test * Checking output from pkg-config gsl * Checking output from pkg-config gsl - 2 * Checking output from pkg-config gsl - 3 * Test with pkg-config * Testing pkgconfig path + removed exporting ld path * More pkg-config testing * More pkg-config testing * More pkg-config testing * More pkg-config testing * Testing after candidate fixs * Cleaned up recipe after successful tests for GSL, added ocamlfind package to opam * Updated PhyloCSF archive to new release that fixes makefile for new compilers * Cleanup, candidate for final recipe 1 * Added gsl to runtime to fix missing gsl shared library in tests * Removed the accidental 0 that I added at the end of build.sh ... * Added test files to source_files in metal.yaml test section * Manually moved file required for test in bin, less clean but otherwise mulled-build fails as test file is missing * woops * Fix attempt for test file * Removed test as it required a file and failed in mulled-build since the file was not present * I don't know why tests are failing * Removed test at the moment * First attempt at implementing tests properly * Second attempt at implementing tests properly * Updated test * Trying to understand testing environment * Test with * Test with 2 * Test with PREFIX 3 * Tentative fix to build on OSX * Update meta.yaml
BiocondaBot
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Jan 15, 2020
Merge PR #19753, commits were: * Update meta.yaml * Update build.sh for QuantWiz_IQ Adding escape "\" character to fix short wrapper part in the recipe * Merge pull request #4 from bioconda/master Sync * Merge pull request #3 from bioconda/master merge * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #2 from bioconda/master Updating repo to origin * Merge pull request #1 from bioconda/master updated from bioconda in fork
BiocondaBot
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Jan 18, 2020
Merge PR #19810, commits were: * add abricate * Merge pull request #6 from liaochenlanruo/master update pgcgap branch * Merge pull request #5 from bioconda/master update local files * add gubbins 2.3.4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * add gubbins 2.3.4 * add gubbins * combination of roary and orthofinder * Update meta.yaml * Merge pull request #4 from liaochenlanruo/master update local branch * Merge pull request #3 from bioconda/master update local fork * Merge pull request #2 from bioconda/master update fork * Update meta.yaml * Update meta.yaml * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master update local recipes
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Jan 21, 2020
Merge PR bioconda#19753, commits were: * Update meta.yaml * Update build.sh for QuantWiz_IQ Adding escape "\" character to fix short wrapper part in the recipe * Merge pull request bioconda#4 from bioconda/master Sync * Merge pull request bioconda#3 from bioconda/master merge * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request bioconda#2 from bioconda/master Updating repo to origin * Merge pull request bioconda#1 from bioconda/master updated from bioconda in fork
jvanheld
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Jan 21, 2020
Merge PR bioconda#19810, commits were: * add abricate * Merge pull request bioconda#6 from liaochenlanruo/master update pgcgap branch * Merge pull request bioconda#5 from bioconda/master update local files * add gubbins 2.3.4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * add gubbins 2.3.4 * add gubbins * combination of roary and orthofinder * Update meta.yaml * Merge pull request bioconda#4 from liaochenlanruo/master update local branch * Merge pull request bioconda#3 from bioconda/master update local fork * Merge pull request bioconda#2 from bioconda/master update fork * Update meta.yaml * Update meta.yaml * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request bioconda#1 from bioconda/master update local recipes
BiocondaBot
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Jan 23, 2020
Merge PR #19905, commits were: * Merge branch 'master' into pgcgap * update pgcgap to v1.0.10 * add abricate * Merge pull request #6 from liaochenlanruo/master update pgcgap branch * Merge pull request #5 from bioconda/master update local files * add gubbins 2.3.4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * add gubbins 2.3.4 * add gubbins * combination of roary and orthofinder * Update meta.yaml * Merge pull request #4 from liaochenlanruo/master update local branch * Merge pull request #3 from bioconda/master update local fork * Merge pull request #2 from bioconda/master update fork * Update meta.yaml * Update meta.yaml * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master update local recipes
BiocondaBot
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Jan 24, 2020
Merge PR #13363, commits were: * Update meta.yaml * Merge branch 'master' into intlim * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of github.com:abotzki/bioconda-recipes * Merge pull request #6 from bioconda/master merge from bioconda master * some cleanups * build requirements removed and LICENSE.txt added * Merge branch 'master' of github.com:abotzki/bioconda-recipes * Merge pull request #5 from bioconda/master merge from bioconda master * Merge pull request #4 from bioconda/master merge from bioconda master * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes into intlim * Merge branch 'master' of github.com:abotzki/bioconda-recipes into intlim * Merge pull request #3 from bioconda/master merge from bioconda * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes into intlim * correct URL and license * add missing packages * typo corrected * Merge branch 'master' of github.com:abotzki/bioconda-recipes into intlim * Merge pull request #2 from bioconda/master merge from bioconda master * add initial version of intlim * scikit-learn added * noarch section added * new recipe mofapy * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master merge from master
BiocondaBot
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Mar 10, 2020
Merge PR #20792, commits were: * Update meta.yaml * Merge branch 'master' into pgcgap * Update PGCGAP to v1.0.11 * Merge branch 'pgcgap' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * canu>=1.8 * Merge branch 'master' into pgcgap * Update meta.yaml * add modeltest-ng and raxml-ng * Merge branch 'master' into pgcgap * add circlator and unicycler * Merge branch 'master' into pgcgap * update pgcgap to v1.0.10 * add abricate * Merge pull request #6 from liaochenlanruo/master update pgcgap branch * Merge pull request #5 from bioconda/master update local files * add gubbins 2.3.4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * add gubbins 2.3.4 * add gubbins * combination of roary and orthofinder * Update meta.yaml * Merge pull request #4 from liaochenlanruo/master update local branch * Merge pull request #3 from bioconda/master update local fork * Merge pull request #2 from bioconda/master update fork * Update meta.yaml * Update meta.yaml * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master update local recipes
BiocondaBot
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Mar 24, 2020
Merge PR #21021, commits were: * Update meta.yaml * Merge branch 'master' into pgcgap * Update PGCGAP to v1.0.11 * Merge branch 'pgcgap' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * canu>=1.8 * Merge branch 'master' into pgcgap * Update meta.yaml * add modeltest-ng and raxml-ng * Merge branch 'master' into pgcgap * add circlator and unicycler * Merge branch 'master' into pgcgap * update pgcgap to v1.0.10 * add abricate * Merge pull request #6 from liaochenlanruo/master update pgcgap branch * Merge pull request #5 from bioconda/master update local files * add gubbins 2.3.4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * add gubbins 2.3.4 * add gubbins * combination of roary and orthofinder * Update meta.yaml * Merge pull request #4 from liaochenlanruo/master update local branch * Merge pull request #3 from bioconda/master update local fork * Merge pull request #2 from bioconda/master update fork * Update meta.yaml * Update meta.yaml * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master update local recipes
BiocondaBot
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Mar 24, 2020
Merge PR #21057, commits were: * A new recipe for BtToxin_scanner * Merge pull request #9 from bioconda/master update local * Merge pull request #7 from bioconda/master update local master * Merge pull request #5 from bioconda/master update local files * Merge pull request #3 from bioconda/master update local fork * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master update local recipes
BiocondaBot
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Apr 13, 2020
Merge PR #21459, commits were: * Update meta.yaml * Merge branch 'master' into pgcgap * Update PGCGAP to v1.0.11 * Merge branch 'pgcgap' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * canu>=1.8 * Merge branch 'master' into pgcgap * Update meta.yaml * add modeltest-ng and raxml-ng * Merge branch 'master' into pgcgap * add circlator and unicycler * Merge branch 'master' into pgcgap * update pgcgap to v1.0.10 * add abricate * Merge pull request #6 from liaochenlanruo/master update pgcgap branch * Merge pull request #5 from bioconda/master update local files * add gubbins 2.3.4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * add gubbins 2.3.4 * add gubbins * combination of roary and orthofinder * Update meta.yaml * Merge pull request #4 from liaochenlanruo/master update local branch * Merge pull request #3 from bioconda/master update local fork * Merge pull request #2 from bioconda/master update fork * Update meta.yaml * Update meta.yaml * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master update local recipes
BiocondaBot
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Apr 19, 2020
Merge PR #21599, commits were: * Update meta.yaml * Merge branch 'master' into pgcgap * Update PGCGAP to v1.0.11 * Merge branch 'pgcgap' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * canu>=1.8 * Merge branch 'master' into pgcgap * Update meta.yaml * add modeltest-ng and raxml-ng * Merge branch 'master' into pgcgap * add circlator and unicycler * Merge branch 'master' into pgcgap * update pgcgap to v1.0.10 * add abricate * Merge pull request #6 from liaochenlanruo/master update pgcgap branch * Merge pull request #5 from bioconda/master update local files * add gubbins 2.3.4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * add gubbins 2.3.4 * add gubbins * combination of roary and orthofinder * Update meta.yaml * Merge pull request #4 from liaochenlanruo/master update local branch * Merge pull request #3 from bioconda/master update local fork * Merge pull request #2 from bioconda/master update fork * Update meta.yaml * Update meta.yaml * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master update local recipes
BiocondaBot
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Jun 19, 2020
Merge PR #22707, commits were: * Update meta.yaml * Update meta.yaml * Update meta.yaml * Merge branch 'master' into pgcgap * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Debug why there are python host dependencies getting pulled in * Update meta.yaml * Update pgcgap to v1.0.18 * Merge pull request #16 from bioconda/master update local master * Merge pull request #14 from bioconda/master Update local master * Merge pull request #9 from bioconda/master update local * Merge pull request #7 from bioconda/master update local master * Merge pull request #5 from bioconda/master update local files * Merge pull request #3 from bioconda/master update local fork * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #1 from bioconda/master update local recipes
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Sep 4, 2020
Merge PR #24062, commits were: * Fix my own mistake * Update meta.yaml * Bump java versiona and add javafx lib Tested locally. MALT's bundled JRE actually includes Java 14? ``` openjdk 14.0.2 2020-07-14 OpenJDK Runtime Environment AdoptOpenJDK (build 14.0.2+12) OpenJDK 64-Bit Server VM AdoptOpenJDK (build 14.0.2+12, mixed mode) ``` * Merge pull request #3 from bioconda/master syncing * Update meta.yaml * Update build.sh * Update SHA * Update meta.yaml * Update damageprofiler.py * Merge pull request #2 from bioconda/master Get latest bioconda version * Update meta.yaml * Update damageprofiler.py * Merge pull request #1 from bioconda/master Syncing to get latest base changes
luispedro
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Sep 7, 2020
Merge PR bioconda#24062, commits were: * Fix my own mistake * Update meta.yaml * Bump java versiona and add javafx lib Tested locally. MALT's bundled JRE actually includes Java 14? ``` openjdk 14.0.2 2020-07-14 OpenJDK Runtime Environment AdoptOpenJDK (build 14.0.2+12) OpenJDK 64-Bit Server VM AdoptOpenJDK (build 14.0.2+12, mixed mode) ``` * Merge pull request bioconda#3 from bioconda/master syncing * Update meta.yaml * Update build.sh * Update SHA * Update meta.yaml * Update damageprofiler.py * Merge pull request bioconda#2 from bioconda/master Get latest bioconda version * Update meta.yaml * Update damageprofiler.py * Merge pull request bioconda#1 from bioconda/master Syncing to get latest base changes
martenson
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Sep 7, 2020
# This is the 1st commit message: add recipes for version 1.1.5 of biotransformer use default python wrapper for Java software # This is the commit message bioconda#2: fix version and a remnant of the template # This is the commit message bioconda#3: rename to "proper"?! yml suffix
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May 20, 2021
Merge PR #28586, commits were: * Update meta.yaml * Update PGCGAP to v1.0.29 * Merge branch 'pgcgap' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * Merge branch 'bioconda:master' into pgcgap * Update meta.yaml debug of the main scripts * Update meta.yaml * Merge branch 'pgcgap' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * Update meta.yaml * Update build-fail-blacklist * Merge branch 'master' into pgcgap * Update meta.yaml * Update PGCGAP to v1.0.28 * Update meta.yaml * Merge remote-tracking branch 'upstream/master' into pgcgap * Update pgcgap to v1.0.27 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #3 from bioconda/master Update local * Merge pull request #1 from bioconda/master Update local
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Jun 12, 2021
Merge PR #28908, commits were: * Update meta.yaml * Merge branch 'pgcgap' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * add pgcgap to the BtToxin_Digger repo * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build-fail-blacklist * Update BtToxin_Digger to v1.0.9 * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #3 from bioconda/master Update local * Merge pull request #1 from bioconda/master Update local
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Jul 21, 2021
Merge PR #29575, commits were: * Update meta.yaml add the version number to each dependency * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * Merge branch 'bioconda:master' into master * Update meta.yaml * Merge branch 'pgcgap' of https://github.com/liaochenlanruo/bioconda-recipes into pgcgap * add pgcgap to the BtToxin_Digger repo * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build-fail-blacklist * Update BtToxin_Digger to v1.0.9 * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #3 from bioconda/master Update local * Merge pull request #1 from bioconda/master Update local
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Apr 12, 2022
Merge PR #33790, commits were: * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update PGCGAP to v1.0.34 Specified dependency version numbers to spend less memory when performing recipe testing. * update pgcgap build number specify the version of all dependences to occupy less memory * Update build number add dependencies * Merge branch 'master' into pgcgap3 * Merge branch 'bioconda:master' into master * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build-fail-blacklist remove PGCGAP * Update meta.yaml * Merge branch 'master' into pgcgap3 * Merge branch 'bioconda:master' into master * Remove some dependencies to solve error code 137 * Update PGCGAP to v1.0.33 * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #3 from bioconda/master Update local * Merge pull request #1 from bioconda/master Update local
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Apr 26, 2022
Merge PR #34517, commits were: * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add new package mgca * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #3 from bioconda/master Update local * Merge pull request #1 from bioconda/master Update local
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Apr 28, 2022
Merge PR #34556, commits were: * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update dependence * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #3 from bioconda/master Update local * Merge pull request #1 from bioconda/master Update local
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Oct 29, 2022
Merge PR #37080, commits were: * Update meta.yaml * Update meta.yaml * Update meta.yaml * Merge branch 'master' into master * Merge branch 'master' into master * Merge pull request #8 from marcDabad/cvlr_package new emas commit * new emas commit * Merge pull request #7 from marcDabad/cvlr_package fix variable * fix variable * Merge branch 'master' into master * Merge pull request #6 from marcDabad/cvlr_package gcc 2 cc * gcc 2 cc * Merge branch 'master' into master * Merge pull request #5 from marcDabad/cvlr_package passes tests in local * passes tests in local * Merge branch 'master' into master * Merge pull request #4 from marcDabad/cvlr_package cc * cc * Merge pull request #3 from marcDabad/cvlr_package Cvlr package * Merge branch 'master' into master * Merge branch 'cvlr_package' of https://github.com/marcDabad/bioconda-recipes into cvlr_package * cvlr_recipe * Merge pull request #2 from marcDabad/cvlr_package Cvlr package * Merge branch 'master' into cvlr_package * Merge pull request #1 from bioconda/master update * cvlr_recipe
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We need to find a way to activate DB_File when building Perl. We might need to package BerkeleyDB for this.
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