Update: htslib, samtools, bcftools to 1.5 #5049
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Update samtools, bcftools and htslib to latest 1.5 release, including fixes for samtools multithread index problems. Bumps pysam requirements to be compatible with latest release.
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This seems to have broken samtools for me: |
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Michael -- sorry about the issue. Can you try installing samtools with conda-forge included: bioconda now requires conda-forge and the conda-forge version of bzip2 uses shared libraries, while the one in the main channel uses a static library. Since it was compiled against the shared library version you need to also have than included in your environment. Hope this fixes it for you. |
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How embarrassing! I made a fresh Anaconda install today, and somehow I managed to screw up the order of channels in my .condarc file. Everything works perfectly :-) |
karel-brinda
pushed a commit
that referenced
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Jul 3, 2017
Update samtools, bcftools and htslib to latest 1.5 release, including fixes for samtools multithread index problems. Bumps pysam requirements to be compatible with latest release.
karel-brinda
pushed a commit
that referenced
this pull request
Jul 3, 2017
* RNFtools 0.3.3.1 * Try to fix Travis PR OS X problem * Try not to install reportlab * Try to install older Reportlab * clean blacklist 2 (#5018) * remove old stuff from blacklist * build r-readbrukerflexdata & r-readmzxmldata * build r-maldiquantforeign * add rematch2 lib using conda skeleton (#4829) * add kernsmooth dep to dupradar (#5023) * update csvtk to v0.9.0 (#5025) * Add MrBayes (#5024) * Add MrBayes * Work around missing `ssh` and `rsh` on linux docker * Run `make clean` between mpi/no-mpi builds * mpirun test needs `allow-run-as-root` flag for docker * More trying to get mpirun to comply on the docker image * Something in bioconda chain breaks `test: requires: - conda` * Pin readline * Disable `conda inspect` tests These seem to be broken in the bioconda toolchain setup. Sometimes it works, sometimes it doesn't. * new recipe for CRISPResso 1.0.6 (#5028) * clean blacklist 3 (#5022) * build bioconductor-cummerbund * build r-ks on linux * Add recipe for gmap 2015.12.31. (#5031) * clean blacklist 4 (#5030) * build r-rainbow & r-hdrcde * clean r-rainbow recipe * use extended-base on r-rainbow * update & build bioconductor-bubbletree * use extended-base on bioconductor-bubbletree * Added new recipe for cmv (#5020) * Added new recipe for cmv * Pinned gmp, removed perl dependency * add perl * Increased stack version dependency * Added cairo dependency * Added pango dependency * Updated to cmv version 1.0.2 * Fixed test command * add pango and cairo as run-time dep as well * Added additional dependencies * Added dependencies * Added libxext * JSON Collect Data Source: update (#5032) * JSON Collect Data Source Extension of the [json_data_source](https://github.com/mdshw5/galaxy-json-data-source) tool. It allows to handle archives (gz, bz2, tar, and zip) organizing their content in a collection. Reference [https://github.com/fabio-cumbo/galaxy-json-collect-data-source](https:/ /github.com/fabio-cumbo/galaxy-json-collect-data-source) * JSON Collect Data Source update 20170619 git_url fixed * JSON Collect Data Source update 20170619 git_rev fixed * JSON Collect Data Source update 20170619 replaced [git_url, git_dev] with [fn, url, md5] * JSON Collect Data Source update 20170620 fixed “imports” under “test” * JSON Collect Data Source update 20170622 From module to script to use it directly under the Galaxy command tag in tool xml schema * JSON collect data source: update (#5034) * JSON Collect Data Source Extension of the [json_data_source](https://github.com/mdshw5/galaxy-json-data-source) tool. It allows to handle archives (gz, bz2, tar, and zip) organizing their content in a collection. Reference [https://github.com/fabio-cumbo/galaxy-json-collect-data-source](https:/ /github.com/fabio-cumbo/galaxy-json-collect-data-source) * JSON Collect Data Source update 20170619 git_url fixed * JSON Collect Data Source update 20170619 git_rev fixed * JSON Collect Data Source update 20170619 replaced [git_url, git_dev] with [fn, url, md5] * JSON Collect Data Source update 20170620 fixed “imports” under “test” * JSON Collect Data Source update 20170622 From module to script to use it directly under the Galaxy command tag in tool xml schema * JSON Collect Data Source update 20170622 Fixed version number * Update: fgbio, bcbio (#5037) - fgbio: latest release to avoid problems with temporary directories and duplex reads fulcrumgenomics/fgbio#256 fulcrumgenomics/fgbio#257 - bcbio: work around issue with google_compute_engine imports on Travis builds by avoiding global import of boto * bump fwdpy11 to 0.1.2 (#4997) * bump fwdpy11 to 0.1.2 * remove old fwdpy11 recipes * Crispresso (#5040) * new recipe for CRISPResso 1.0.6 * CRISPResso 1.0.6 * CRISPResso dep * Bug fix of 0.5.6 (#4951) I built a new tar ball of mageck source file to fix a bug existing in previous versions. Future updates will b assigned a new version number. * bumped build number (#5035) bumped build number so updated plugins will be pulled during build. * ensembl_vep: bumped subversion (#5036) * Add MACOSX_DEPLOYMENT_TARGET to env matrix. (#5039) * Add MACOSX_DEPLOYMENT_TARGET to env matrix. * Typo. * add peakachu (#5038) adds package of peakachu peak caller * Bump cutadapt to 1.14 (#4990) * clean blacklist 5 (#5041) * build r-spp * build bioconductor-motiv on linux * build bioconductor-motifstack on linux * build bioconductor-motifbreakr on linux * build r-multicool on osx * Update mysqlclient (#5043) * update mysqlclient * remove from blacklisted * Add InDelFixer v1.1 (#5029) * Add recipe for InDelFixer 1.1 * Change java-jdk for openjdk * Fix wrapper file name * Add PhyML (#5033) * Add PhyML * Add PhyML 3.2.0 * Pin openmpi to 2.* * Pin beagle-lib to >=2.1.2-7 For some odd reason, the test stage likes to install other package versions, like in this case the 2.1.2-1 which has different requirements (doesn't need libtool), leading to linking failure. * Pinning to build numbers doesn't seem to work? * Add missing patch * Add ARB (#4952) * Use openmotif-dev during build * Fix relative paths in Makefile * Change all absolute tool paths * Don't use `gsed` on OSX * Request sed >= 4.4 to get the one from conda-forge * Remove -w from perl script calls * Require `readline` needed by MrBayes * Fix rpath * Move tests to `run_test.sh` * Pin things depending on broken gettext * Exclude broken perl version * Pin glib to 2.51.* * version 1.0.7 (#5044) * Update: bcbio-vm with boto import fixes (#5045) Additional work on avoiding boto import errors on Travis * Update: htslib, samtools, bcftools to 1.5 (#5049) Update samtools, bcftools and htslib to latest 1.5 release, including fixes for samtools multithread index problems. Bumps pysam requirements to be compatible with latest release. * address #4958 (#5048) fix abyss * Bump Picopore to 1.1.5 (#5046) * Mothur update (#5050) * updated mothur to latest version 1.39.5 * added summary line * updated the patch file to reflect current version of mothur * Update htslib to latest 1.5 release (#5052) Bumps CONDA_HTSLIB and re-builds packages that reference it. Pin pysam to CONDA_HTSLIB. Fixes bcbio/bcbio-nextgen#1987 * Add missing X library to arb-bio (#5056) * Snakemake 3.13.3 (#5042) * Update: fgbio with duplex fixes (#5059) fulcrumgenomics/fgbio#257 * ngmlr 0.2.5 (#5054) * Update version and sha1 (#5060) * Nglview 0.6.4 (#5057) * nglivew: 0.6.4 * Update meta.yaml (#5068) * Update GMTK build to use logp table optimisations (#5064) * Change GMTK to use logp optimisation for speed * Correct logp specification option * Update to v1.4.0 (#5070) * nextflow 0.25.1 (#5063) * Added netReg as new bioconda recipe (#4754) * update askocli to 0.3.4 (#5069) * update askocli to 0.3.4 * update md5sum * Update: Toil, VariantBam (#5073) - Toil: include fixes for PBSPro, AWS and local symlink runs - VariantBam: QC flagging downsampled reads (walaj/VariantBam#9) and large VCF line support (walaj/VariantBam#10) [lint skip uses_git_url for recipes/variantbam] * Update: VariantBam with QC fail marking fixes (#5078) [lint skip uses_git_url for recipes/variantbam] * Kraken ea (#5071) * Added kraken-ea recipe * Updated build flags * Updated build flags * Updated the release details * Updated build script * Updated yaml * Updated yaml * Updated yaml * Updated build * Changes to build and meta.yaml as suggested during pull request * meta.yaml Jellyfish version fixed * More build changes to remove libexec * Fixed variable issue in build.sh * fluff version bump (#5076) * Gimme deps (#5080) * added gimmemotifs dependencies * configparser already there * Bump version of pymzml to 0.7.8 (#5082) * Bump nanoraw to 0.5 (#5083) * Bump fast5 (#5084) * Bump nanopolish to 0.7.0 (#5085) * added a new patch to fix Rfam_for_miRDeep.fa location (#5075) * added a new patch to fix Rfam_for_miRDeep.fa location * increased build * Update: Platypus to support hg38 (#5087) Fixes bcbio/bcbio-nextgen#1988 * Ncbi genome download 0.2.4 (#5089) * Bump ncbi-genome-download to 0.2.4 * pin jpeg lib on gnuplot recipe (#5065) * pin jpeg lib * create test data on-the-fly * Kraken ea (#5092) * Added kraken-ea recipe * Updated build flags * Updated build flags * Updated the release details * Updated build script * Updated yaml * Updated yaml * Updated yaml * Updated build * Changes to build and meta.yaml as suggested during pull request * meta.yaml Jellyfish version fixed * More build changes to remove libexec * Fixed variable issue in build.sh * Minor edits to run_test.pl * removing hlaprofiler * Adding recipe * Removing hlaprofiler again * Cleaned up meta.yml * Added gcc dependency * Reverting meta.yaml to original * Updated to have gcc dependency * Reverting to original meta.yaml * Adding gcc dependencies * Version bump synapseclient, thanks @chapmanb (#5079) * hlaprofiler (#5094) * Minor edits to run_test.pl * removing hlaprofiler * Adding hlaprofiler recipe * Add requires to test * Updated tests * Updated release and test cases * Update lofreq to 2.1.3.1 with python 3 support (#5088) * Update lofreq to 2.1.3.1 with python 3 support * Linting fails: add md5 sums. * Lint fails on 2.1.2 (has md5 requirement been added more recently?): add hashes there
karel-brinda
pushed a commit
that referenced
this pull request
Jul 5, 2017
* RNFtools 0.3.3.1 * Try to fix Travis PR OS X problem * Try not to install reportlab * Try to install older Reportlab * clean blacklist 2 (#5018) * remove old stuff from blacklist * build r-readbrukerflexdata & r-readmzxmldata * build r-maldiquantforeign * add rematch2 lib using conda skeleton (#4829) * add kernsmooth dep to dupradar (#5023) * update csvtk to v0.9.0 (#5025) * Add MrBayes (#5024) * Add MrBayes * Work around missing `ssh` and `rsh` on linux docker * Run `make clean` between mpi/no-mpi builds * mpirun test needs `allow-run-as-root` flag for docker * More trying to get mpirun to comply on the docker image * Something in bioconda chain breaks `test: requires: - conda` * Pin readline * Disable `conda inspect` tests These seem to be broken in the bioconda toolchain setup. Sometimes it works, sometimes it doesn't. * new recipe for CRISPResso 1.0.6 (#5028) * clean blacklist 3 (#5022) * build bioconductor-cummerbund * build r-ks on linux * Add recipe for gmap 2015.12.31. (#5031) * clean blacklist 4 (#5030) * build r-rainbow & r-hdrcde * clean r-rainbow recipe * use extended-base on r-rainbow * update & build bioconductor-bubbletree * use extended-base on bioconductor-bubbletree * Added new recipe for cmv (#5020) * Added new recipe for cmv * Pinned gmp, removed perl dependency * add perl * Increased stack version dependency * Added cairo dependency * Added pango dependency * Updated to cmv version 1.0.2 * Fixed test command * add pango and cairo as run-time dep as well * Added additional dependencies * Added dependencies * Added libxext * JSON Collect Data Source: update (#5032) * JSON Collect Data Source Extension of the [json_data_source](https://github.com/mdshw5/galaxy-json-data-source) tool. It allows to handle archives (gz, bz2, tar, and zip) organizing their content in a collection. Reference [https://github.com/fabio-cumbo/galaxy-json-collect-data-source](https:/ /github.com/fabio-cumbo/galaxy-json-collect-data-source) * JSON Collect Data Source update 20170619 git_url fixed * JSON Collect Data Source update 20170619 git_rev fixed * JSON Collect Data Source update 20170619 replaced [git_url, git_dev] with [fn, url, md5] * JSON Collect Data Source update 20170620 fixed “imports” under “test” * JSON Collect Data Source update 20170622 From module to script to use it directly under the Galaxy command tag in tool xml schema * JSON collect data source: update (#5034) * JSON Collect Data Source Extension of the [json_data_source](https://github.com/mdshw5/galaxy-json-data-source) tool. It allows to handle archives (gz, bz2, tar, and zip) organizing their content in a collection. Reference [https://github.com/fabio-cumbo/galaxy-json-collect-data-source](https:/ /github.com/fabio-cumbo/galaxy-json-collect-data-source) * JSON Collect Data Source update 20170619 git_url fixed * JSON Collect Data Source update 20170619 git_rev fixed * JSON Collect Data Source update 20170619 replaced [git_url, git_dev] with [fn, url, md5] * JSON Collect Data Source update 20170620 fixed “imports” under “test” * JSON Collect Data Source update 20170622 From module to script to use it directly under the Galaxy command tag in tool xml schema * JSON Collect Data Source update 20170622 Fixed version number * Update: fgbio, bcbio (#5037) - fgbio: latest release to avoid problems with temporary directories and duplex reads fulcrumgenomics/fgbio#256 fulcrumgenomics/fgbio#257 - bcbio: work around issue with google_compute_engine imports on Travis builds by avoiding global import of boto * bump fwdpy11 to 0.1.2 (#4997) * bump fwdpy11 to 0.1.2 * remove old fwdpy11 recipes * Crispresso (#5040) * new recipe for CRISPResso 1.0.6 * CRISPResso 1.0.6 * CRISPResso dep * Bug fix of 0.5.6 (#4951) I built a new tar ball of mageck source file to fix a bug existing in previous versions. Future updates will b assigned a new version number. * bumped build number (#5035) bumped build number so updated plugins will be pulled during build. * ensembl_vep: bumped subversion (#5036) * Add MACOSX_DEPLOYMENT_TARGET to env matrix. (#5039) * Add MACOSX_DEPLOYMENT_TARGET to env matrix. * Typo. * add peakachu (#5038) adds package of peakachu peak caller * Bump cutadapt to 1.14 (#4990) * clean blacklist 5 (#5041) * build r-spp * build bioconductor-motiv on linux * build bioconductor-motifstack on linux * build bioconductor-motifbreakr on linux * build r-multicool on osx * Update mysqlclient (#5043) * update mysqlclient * remove from blacklisted * Add InDelFixer v1.1 (#5029) * Add recipe for InDelFixer 1.1 * Change java-jdk for openjdk * Fix wrapper file name * Add PhyML (#5033) * Add PhyML * Add PhyML 3.2.0 * Pin openmpi to 2.* * Pin beagle-lib to >=2.1.2-7 For some odd reason, the test stage likes to install other package versions, like in this case the 2.1.2-1 which has different requirements (doesn't need libtool), leading to linking failure. * Pinning to build numbers doesn't seem to work? * Add missing patch * Add ARB (#4952) * Use openmotif-dev during build * Fix relative paths in Makefile * Change all absolute tool paths * Don't use `gsed` on OSX * Request sed >= 4.4 to get the one from conda-forge * Remove -w from perl script calls * Require `readline` needed by MrBayes * Fix rpath * Move tests to `run_test.sh` * Pin things depending on broken gettext * Exclude broken perl version * Pin glib to 2.51.* * version 1.0.7 (#5044) * Update: bcbio-vm with boto import fixes (#5045) Additional work on avoiding boto import errors on Travis * Update: htslib, samtools, bcftools to 1.5 (#5049) Update samtools, bcftools and htslib to latest 1.5 release, including fixes for samtools multithread index problems. Bumps pysam requirements to be compatible with latest release. * address #4958 (#5048) fix abyss * Bump Picopore to 1.1.5 (#5046) * Mothur update (#5050) * updated mothur to latest version 1.39.5 * added summary line * updated the patch file to reflect current version of mothur * Update htslib to latest 1.5 release (#5052) Bumps CONDA_HTSLIB and re-builds packages that reference it. Pin pysam to CONDA_HTSLIB. Fixes bcbio/bcbio-nextgen#1987 * Add missing X library to arb-bio (#5056) * Snakemake 3.13.3 (#5042) * Update: fgbio with duplex fixes (#5059) fulcrumgenomics/fgbio#257 * ngmlr 0.2.5 (#5054) * Update version and sha1 (#5060) * Nglview 0.6.4 (#5057) * nglivew: 0.6.4 * Update meta.yaml (#5068) * Update GMTK build to use logp table optimisations (#5064) * Change GMTK to use logp optimisation for speed * Correct logp specification option * Update to v1.4.0 (#5070) * nextflow 0.25.1 (#5063) * Added netReg as new bioconda recipe (#4754) * update askocli to 0.3.4 (#5069) * update askocli to 0.3.4 * update md5sum * Update: Toil, VariantBam (#5073) - Toil: include fixes for PBSPro, AWS and local symlink runs - VariantBam: QC flagging downsampled reads (walaj/VariantBam#9) and large VCF line support (walaj/VariantBam#10) [lint skip uses_git_url for recipes/variantbam] * Update: VariantBam with QC fail marking fixes (#5078) [lint skip uses_git_url for recipes/variantbam] * Kraken ea (#5071) * Added kraken-ea recipe * Updated build flags * Updated build flags * Updated the release details * Updated build script * Updated yaml * Updated yaml * Updated yaml * Updated build * Changes to build and meta.yaml as suggested during pull request * meta.yaml Jellyfish version fixed * More build changes to remove libexec * Fixed variable issue in build.sh * fluff version bump (#5076) * Gimme deps (#5080) * added gimmemotifs dependencies * configparser already there * Bump version of pymzml to 0.7.8 (#5082) * Bump nanoraw to 0.5 (#5083) * Bump fast5 (#5084) * Bump nanopolish to 0.7.0 (#5085) * added a new patch to fix Rfam_for_miRDeep.fa location (#5075) * added a new patch to fix Rfam_for_miRDeep.fa location * increased build * Update: Platypus to support hg38 (#5087) Fixes bcbio/bcbio-nextgen#1988 * Ncbi genome download 0.2.4 (#5089) * Bump ncbi-genome-download to 0.2.4 * pin jpeg lib on gnuplot recipe (#5065) * pin jpeg lib * create test data on-the-fly * Kraken ea (#5092) * Added kraken-ea recipe * Updated build flags * Updated build flags * Updated the release details * Updated build script * Updated yaml * Updated yaml * Updated yaml * Updated build * Changes to build and meta.yaml as suggested during pull request * meta.yaml Jellyfish version fixed * More build changes to remove libexec * Fixed variable issue in build.sh * Minor edits to run_test.pl * removing hlaprofiler * Adding recipe * Removing hlaprofiler again * Cleaned up meta.yml * Added gcc dependency * Reverting meta.yaml to original * Updated to have gcc dependency * Reverting to original meta.yaml * Adding gcc dependencies * Version bump synapseclient, thanks @chapmanb (#5079) * hlaprofiler (#5094) * Minor edits to run_test.pl * removing hlaprofiler * Adding hlaprofiler recipe * Add requires to test * Updated tests * Updated release and test cases * Update lofreq to 2.1.3.1 with python 3 support (#5088) * Update lofreq to 2.1.3.1 with python 3 support * Linting fails: add md5 sums. * Lint fails on 2.1.2 (has md5 requirement been added more recently?): add hashes there * RNFtools 0.3.1.2
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I also had this problem and @chapmanb's solution worked for me. @micknudsen, others: what's the proper order in my .condarc to prevent this from happening? Currently, mine is: Thanks. |
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@stephenturner The correct order is |
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Update samtools, bcftools and htslib to latest 1.5 release, including
fixes for samtools multithread index problems. Bumps pysam requirements
to be compatible with latest release.