Trinity #10419
Merged
Trinity #10419
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
* add convert_zero_one_based * remove unecessary tests * test import
* gembs: passes a mulled build * correcting dependencies * gembs: passes a mulled build * correcting dependencies * pointing to the current gem3-mapper instead of a custom version * removing openssl * gembs: passes a mulled build * correcting dependencies * pointing to the current gem3-mapper instead of a custom version * removing openssl * starting build at 0 * Changing to the main repository instead of the testing fork
* update to new version the old version had a bug whereby some reads were dropped. See mourisl/Rcorrector#12 * remove recipe from blacklist * Update meta.yaml * try adding flags per comment from @jpuritz * fix makefile
* bump for alevin hotfix * Update meta.yaml Put md5sum for the zip, not .tar.gz. Correct that.
Add missing dependency perl-io-uncompress-gunzip. Support osx.
bioconda#10105) * updating to ragout v2.1, should fix the problem with inconsistent newick package versions
* Started work on dialign2 * Fixing build/host * compiler * still compiler error * still * still working on compiler * should be fixed * Fixed typo * desperate measures * typo * whatever * Update meta.yaml * fix hash * freaky circleci, please run * working on paths and exports * still working on paths and exports * still working on paths * last fixes * verylast fixes * verylast fixes? * wtf circleci * wtf circleci aber echt * Fixing license * Working * env vars export * Working on postlink * Working on prelink * Working on env vars * Done? * skipping osx and done i hope * Added pre-unlink and added DOI * Fixing exports * Removed unnecessary scripts, added wrapper * Added patch and sed workaround for env var DIALIGN2_DIR * Fixing sed command * Fixing sed command again * I hate sed * fixed typo and eyecandy
* Remove various packages from the blacklist
* eqtlbma needs to always have openblas included
* Patch mamotif so it uses matplotlib.use('Agg') early on
* Skip eqtlbma on OSX due to openmp
* Add r-bipartite * removed 2nd url
* Add r-phylomeasures * removed 2nd url
* Bump perl-file-path * Small fixes
* Update primer3 to v2.4.0 * [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [x] This PR updates an existing recipe. * [ ] This PR does something else (explain below). Bump primer3 to `v2.4.0`. * Review fixups for Update primer3 to v2.4.0
* Add r-phylosignal * Removed fn: * removed all win * fixed meta.yaml; ade4 now updated to 1.7_11
* Add r-coenocliner * modified maintainers
* add msisensor * skip macos * change include and lib * fix ncurse * add tinfo * add cpath * add LIBRARY_PATH
This version provides a fix for possible deadlock on cloud-based docker env.
* Add r-ggrasp * trivial change to restart checks now the r-bgmm is on conda-forge
* remove a few things from the blacklist * Try something for osx * skip xatlas on osx
* Fix perl-image-size * Fix perl-aceperl * Add perl-cache-cache * Add perl-ipc-sharelite * Add perl-digest-sha1
* Remove packages from the blacklist * Fix fermi on osx I hope * Ah, only gnu assumes inline functions are static * preseq 2.0.3 includes the wrong header for proper building on newer OSX versions. Try to cxxflags around this. * Skip preseq on OSX, clang doesn't like the older headers
* Added recipe prototype for pymisc-utils * Updated build dependencies * Updated repo url * Fixed copying of executables * Added dependency * Minor fix * Skip python 2
* idr: push version to 2.0.4.2
* OMERO.py 5.4.7 * Bump version in setup.py to 5.4.7
* Update helperlibs to release-0-1-9 * use pip
* Update binsanity to 0.2.6.3 * add noarch
* update bioconvert to v0.2.0
* unblacklist * lint * bump * typo * force version * fix augustus 3.2.3 * bump * bump more * disable repeatmasker until prl package removed from bioconda * mac perms * thanks @bgruening :) * mac fix * mac fix * max fix * mac fix * typo * typo * trigger new test * delay repeatmasker * mac perms
* Fix perl-date-manip * Fix perl-env-path * Unblacklist * Fix perl-json-parse * Unblacklist * Remove older perl-json-parse * fix build number
* Add MOB-suite recipe to the channel.MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies * updated recipe to download from URL instead of github * build python version requirement defined (python >=3.4) * added build number * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added test statement (import) * added test statement (import) * added the new repository and py36 only compile * made requested corrections by daler. Corrected build number and package string * Small fixes * revert deleted row * New version, fixed sum bugs and improved stability * Updated 1.4.8 version. The str to int casting issues corrected for the --min... parameters * new version should reset the build number to 0
* nanopolish outof blacklist * openmp * cxx compiler * config for build * compiler mess * skip linting for compilers to accept the hack * Update meta.yaml * of course old style needs libgcc
* Remove various recipes from the black list * apoc needs fortran * skip OSX with agg
* Add r-softimpute * Add bioconductor-zinbwave * Fixed errors detected during linting * Added the 'extras' section * Removed Windows-specific lines from the r-softimpute recipe * Forgot to remove some Windows-specific lines * Fixed r-softimpute build.sh * Fix source url * Remove r-softimpute * Add gsl dependency * Fix gsl version * skip macOS build
* Adding a recipe for ksw * lint? * use tag as PCK_VERSION * more * one commit to rule them all
…t can fall back on the host installation, but when running in a biocontainer it only has access to the busybox version which lacks some necessary options. (bioconda#10383)
* Fix perl-text-nsp * Fix perl-image-exiftool * Fix perl-test-output * Unblacklist * Fix shebang
* flowtools * Update meta.yaml * skip noarch linting
* Bump perl-parse-yapp * Fix typo
perl-bioperl now available, pin to updated version to get all dependencies in sync. Fixes bioconda#10366
* First version of biobb_common package recipe * Adding build noarch section and removing fn section * Modification in no arch section * Deleting build.sh
* Fix installation for hg19 * Fix hg38 * Fix mm10 * Better syntax
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.
Trinity bioconda update for version 2.8.1