Build packages #4
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Hi Johannes & Hyeshik - I built my packages locally, but am unable to upload to the bioconda channel. The only solution I was able to find for organizations was in this post, but gives me the error Have either of you had luck uploading to the bioconda organization? |
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Hi Ryan, |
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Hmm, still not working for me. I made my own test organization and was able to successfully upload a new package to it, so it seems like things are configured correctly on my machine, at least for organizations created by my user name. I added you as a user with "owner" rights to that new organization, which is unoriginally named "temp" . . . are you able to upload packages there? |
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Yes, I can upload there... |
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Yep, now it works. Thanks! |
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I was trying to figure out how to upload my packages. :) I just successfully finished uploading my packages. Thank you! |
bgruening
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Mar 22, 2016
llvm does not seen to work, trying with gcc under OSX
martin-raden
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Nov 9, 2016
merging bioconda master (trinotate update)
mbargull
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Jan 30, 2018
Update from upstream repo bioconda/bioconda-recipes
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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Dec 17, 2019
Merge PR #19345, commits were: * Update pneumocat recipe to use correct dependencies * Merge branch 'master' of github.com:bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/phac-nml/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge pull request #4 from phac-nml/update-rgi Update rgi * Revert "line fix in bootstrap.py" This reverts commit 5ac1ecd. * move build script into meta.yaml * add preprocessing selector to skip python 2.7 * change python & matplotlib versions; add build.sh file * line fix in bootstrap.py * remove older recipes * move build script into meta * fix build * update meta and build * testing circleci * change build number * change source to github * update dependencies list * first commit
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
jvanheld
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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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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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Apr 21, 2020
Merge PR #21664, commits were: * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of github.com:bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/phac-nml/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge pull request #4 from phac-nml/update-rgi Update rgi * Revert "line fix in bootstrap.py" This reverts commit 5ac1ecd. * move build script into meta.yaml * add preprocessing selector to skip python 2.7 * change python & matplotlib versions; add build.sh file * line fix in bootstrap.py * remove older recipes * move build script into meta * fix build * update meta and build * testing circleci * change build number * change source to github * update dependencies list * first commit
BiocondaBot
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May 1, 2020
Merge PR #21851, commits were: * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of github.com:bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/phac-nml/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge pull request #4 from phac-nml/update-rgi Update rgi * Revert "line fix in bootstrap.py" This reverts commit 5ac1ecd. * move build script into meta.yaml * add preprocessing selector to skip python 2.7 * change python & matplotlib versions; add build.sh file * line fix in bootstrap.py * remove older recipes * move build script into meta * fix build * update meta and build * testing circleci * change build number * change source to github * update dependencies list * first commit
a-solovyev12
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Jun 29, 2020
Merge PR bioconda#21851, commits were: * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of github.com:bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'master' of https://github.com/phac-nml/bioconda-recipes * Merge remote-tracking branch 'upstream/master' * Merge remote-tracking branch 'upstream/master' * Merge pull request #4 from phac-nml/update-rgi Update rgi * Revert "line fix in bootstrap.py" This reverts commit 5ac1ecd. * move build script into meta.yaml * add preprocessing selector to skip python 2.7 * change python & matplotlib versions; add build.sh file * line fix in bootstrap.py * remove older recipes * move build script into meta * fix build * update meta and build * testing circleci * change build number * change source to github * update dependencies list * first commit
BiocondaBot
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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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Hi Hyeshik,
nice work with the new packages! Are you able to build and upload them, or do you want me to do that? We could also try to setup the anaconda build service for linux-64, but so far I did no manage to connect it with github...
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