Manual push containers

[bernt-matthias]

Have some older versions of tools that need containers which can only be built with some additional requirements. I use this issue to keep track of and document transparently .. and someone may push them manually:

• https://toolshed.g2.bx.psu.edu/repos/yguitton/metams_rungc/file/c75532b75ba1
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" bioconductor-metams=1.8.0,bioconductor-xcms=1.46.0,r-batch=1.1_4,r-base=3.4.1,libgfortran=3.0.0,libgfortran4=7.5.0 mulled-build build --verbose --name-override mulled-v2-8e43efd53951b49bbcd3d50a883c93ef9038a927:51a49b963d243ab8961ab7a9d9dd698d7c1c5386-0 --namespace biocontainers
  • I accidentally made this which created a container with a "wrong hash"
  • MetaMS will be added to W4M repo .. so there will be containers for future versions of the tool
• https://toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/file/d7a7ef786fbe
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build bioconductor-msnbase=2.4.0,r-batch=1.1_4,unzip=6.0,libgfortran=3.0.0 --verbose --name-override mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:a76e3a712b8e1271923ac8af141f707635749ba1-0 --namespace biocontainers
  • the container is for an old version of the tool, it is now part of W4M, i.e. containers are generated

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/file/73d82de36369

  • use graphicsmagick 1.3.30 instead of 1.3.23 (strict-channel-priority) NOT SURE IF THIS IS ACCEPTABLE
  • add fortran stuff
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-snow=0.4_2,bioconductor-xcms=3.0.0,bioconductor-camera=1.34.0,bioconductor-multtest=2.28.0,r-batch=1.1_4,graphicsmagick=1.3.30,libgfortran4=7.5.0,libgfortran=3.0.0 --verbose --name-override mulled-v2-47ae9e3c6f99bd09152e04210b86637d4965e446:4cfdd6d3bd6531a1f2bd7e3242faeb6ac32ee26a-0

• https://toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/file/6139bfcc95cb

  • similar to the previous (graphicsmagic update and one additional fortran package)
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-snow=0.4_2,bioconductor-camera=1.32.0,bioconductor-multtest=2.28.0,r-batch=1.1_4,graphicsmagick=1.3.30,libgfortran=3.0.0 --verbose --name-override mulled-v2-a0d3bf2aa6e4255087a5fc18e8881735a726c90b:1c8a57c5aaa02aca792b01093fb76c98c6cca28b-0

The tool is now in w4m, i.e. newer versions have a container

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_summary/file/4c757d1ba7b4
  • add fortran package
  • REPO=quay.io/biocontainers/mulled-v2-a38bda4fc5b4cc0a63ce6b780f67da8c7cbb0d83:d2e54d5d09eb3072e926ccfdc520e9bc0b475f1a-0 DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build bioconductor-camera=1.32.0,r-batch=1.1_4,libgfortran=3.0.0 --verbose --name-override mulled-v2-a38bda4fc5b4cc0a63ce6b780f67da8c7cbb0d83:d2e54d5d09eb3072e926ccfdc520e9bc0b475f1a-0 --namespace biocontainers
  • the tool is now in w4m and newer versions have a container
• https://toolshed.g2.bx.psu.edu/repos/lecorguille/anova/file/102049093b7d
  • add fortran package
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_4,r-venn=1.2,libgfortran=3.0.0 --verbose --name-override mulled-v2-f60562fb6f9f20c9d4fcf547b39a228ac8870642:ce5b3d418fa1abda69d34aec157dd02823d37a9f-0
  • The tool may be added to W4M: move anova tool workflow4metabolomics/tools-metabolomics#286 .. so I hope there will automatically containers from now on

[bgruening]

Done

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/file/23314e1192d4/BC/determine_bc.xml
  • add fortran package
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_4,r-ade4=1.7_8,bioconductor-pcamethods=1.70.0,libgfortran=3.0.0 --verbose --name-override mulled-v2-8768558280a591d3ab2f379cca46dbe488b1f888:65517c174e75921ae331e8147bd728599b285183-0
• https://toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/file/23314e1192d4/BC/batch_correction.xml
  • add fortran
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_4,r-ade4=1.7_8,bioconductor-pcamethods=1.70.0,libgfortran=3.0.0 --verbose --name-override mulled-v2-8768558280a591d3ab2f379cca46dbe488b1f888:65517c174e75921ae331e8147bd728599b285183-0

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/file/acdf51018708
  • add fortran
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_4,bioconductor-ropls=1.10.0,libgfortran=3.0.0 --verbose --name-override mulled-v2-e45958c21042ab0a8f3d351e34852fed27926c05:a784e7e6038229bcd15386f3bef0802488d63e19-0

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/file/fa80bd02055f
  • tool requirements specify no versions, for the mulled command I specify those from my local conda env
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_5,bioconductor-biosigner=1.10.0 --verbose --name-override mulled-v2-0df183b841e99009662386012e97e80cdcedcf0d:0-0

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/file/140290de7986
  • fortran
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r=3.4.1,r-batch=1.1,r-pmcmr=4.1,libgfortran=3.0.0 --verbose --name-override mulled-v2-8b49539da640c8dbf978b3e9c22003a3d0bfc6ba:860661d59d7f5af88409bc3dd35d51489c0994bb-0
• https://toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/file/5687435b182c
  • fortran
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_4,r-pmcmr=4.1,libgfortran=3.0.0 --verbose --name-override mulled-v2-5b179ea0e0f0a70b0c67dcd9062b1d5659da5580:ec5cc94c53fe5e4f2a4ce129c5ffc86411e0dbfe-0

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/mmonsoor/probmetab/file/52b222a626b0
  • add two fortran requirements
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-snow=0.4_3,r-probmetab=1.0,r-batch=1.1_4,libgfortran4=7.5.0,libgfortran=3.0.0 --verbose --name-override mulled-v2-3e559ad6c219caeca1de1cafd40eedafcf400235:c13cadf2a530d5f20a5c311b990e0c63f81b8c4d-0

[bernt-matthias]

• [ ] https://toolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/nmr_bucketing/file/4d5c06b46c2f
  • replace r-pracma 1.8.8 with earliest fron conda-forge
  • add fortran
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_4,r-pracma=2.0.4,libgfortran=3.0.0 --verbose --name-override mulled-v2-256547e9e0aa77fb35d229ae3e4b61520ec3a99f:74e53bb2dadd063d0d06762f07b759328b48f218-0

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/asca/file/93312041f1d5
  • use bioconductor-pcamethods-1.72.0 instead of bioconductor-pcamethods-1.70.0 which was not installable
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_4,r-metstat=1.0,bioconductor-pcamethods=1.72 --verbose --name-override mulled-v2-c3eed2c06f3f3ca2420bf019435b1036f438b348:b9c8c2ff842f63e4e64cfbbdaa79d1280e85fadf-0

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/file/9be4beda6482
  • python=2.7.10 => 2.7.15
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build metaphlan2=2.6.0,bowtie2=2.3.0,python=2.7.15 --verbose --name-override mulled-v2-da271c8774be2b8dbd760259a085347c47897e8b:3eba2b66b7b62c358a394d58655730a65ba3b4c8-0

[bernt-matthias]

• https://toolshed.g2.bx.psu.edu/repos/iuc/humann2/file/cda49fede0c2
  • python=2.7.10 => 2.7.15
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build humann2=0.11.1,bowtie2=2.3.0,metaphlan2=2.6.0,diamond=0.8.24,rapsearch=2.24,python=2.7.15 --verbose --name-override mulled-v2-f925044e44f9f57875127bf77dd748a28bbcc7a5:7e4544174d899742dfdaf98dc51d6669b6f34c2f-0
• https://toolshed.g2.bx.psu.edu/repos/ethevenot/profia/file/de9d1270a9ae
  • added fortran
  • DEST_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest" mulled-build build r-batch=1.1_4,bioconductor-profia=1.4.0,libgfortran=3.0.0 --verbose --name-override mulled-v2-4b4a737b42c5fe89e128023c3def1665ae02bec7:7471307736cd42030614b527879f0a255e0443a3-0