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* update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1 (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336) * Fix various recipes (#11354) * Fix various recipes * Fix more recipes * Various CRAN package fixes, since they all lack license files (#11372) * Various CRAN package fixes, since they all lack license files * Fix the r-dartr recipe * There is a light at the end of the tunnel (#11381) * There is a light at the end of the tunnel * Licenses no longer exist * [BULK] Fixes for R/Bioconductor packages (#11406) * Require `r-base >=3.5` for some packages * Fix various CRAN packages lacking license file * Add missing libnetcdf requirement to bioconductor-mzr * Remove r-alakazam (moved to conda-forge) Fix linting issue: ``` recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating ``` * [BULK] Many R 3.5 only packages (#11410) * Update pinning to R>=3.5 and a few runtime dependencies. * CSAW is R 3.5 only * Packages using beachmat are 3.5 only * Packages using bioconductor-singlecellexperiment are R 3.5 only
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