Andreas Tille pushed to branch master at Debian Blends Team / med
Commits: 69f1c951 by Andreas Tille at 2020-04-23T08:47:25+02:00 Cleanup tasks: Some packages are ported to Python3, some were just wrongly spelled, syntax fixes - - - - - 3 changed files: - tasks/bio - tasks/bio-dev - tasks/cloud Changes: ===================================== tasks/bio ===================================== @@ -288,8 +288,6 @@ Recommends: pizzly Recommends: raxml -Recommends: seqcluster - Recommends: mlv-smile Recommends: cd-hit @@ -419,7 +417,7 @@ Recommends: csb Recommends: diamond-aligner -Recommends: emperor +Recommends: python3-emperor Recommends: euler2, euler-sr @@ -754,7 +752,7 @@ Recommends: metaphlan2 Recommends: metastudent -Suggests: metastudent-data, metastudent-data-2, metastudent-data-3 +Suggests: metastudent-data, metastudent-data-2 Recommends: microbegps @@ -952,7 +950,7 @@ Recommends: python3-pybedtools Recommends: python3-sqt -Recommends: python3-reaper +Recommends: qtlreaper Suggests: python3-tinyalign @@ -1030,12 +1028,6 @@ Suggests: r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-ensembldb, Suggests: r-bioc-go.db -Suggests: r-bioc-org.hs.eg.db, - r-bioc-org.mm.eg.db, - r-bioc-org.dm.eg.db, - r-bioc-org.rn.eg.db, - r-bioc-org.ce.eg.db - Suggests: r-bioc-qusage Suggests: r-cran-qqman @@ -1411,15 +1403,6 @@ Recommends: concavity Recommends: conservation-code Recommends: galaxy -Homepage: http://g2.trac.bx.psu.edu/ -License: MIT -WNPP: 432472 -Pkg-Description: manipulate sequences and annotation files - Galaxy is a web-based tool allowing users to perform operations which - are usually done with command-line interface. Using galaxy, one can - manipulate sequences and annotation files in many formats. Galaxy has - strong ties with the UCSC genome browser, and makes it easy to - visualise modified annotation files as a custom track. Recommends: genographer Homepage: https://sourceforge.net/projects/genographer/ ===================================== tasks/bio-dev ===================================== @@ -20,8 +20,7 @@ Recommends: python3-biopython Suggests: python3-biopython-sql, python-biopython-doc -Suggests: python-cogent -Comment: py2removal +Recommends: python3-cogent3 Suggests: python3-pycosat @@ -29,7 +28,7 @@ Recommends: python3-screed Recommends: python3-cutadapt, python3-dnaio -Suggests: python3-tinyalign +Recommends: python3-tinyalign Recommends: ruby-bio @@ -70,8 +69,7 @@ Recommends: libzerg0-dev, libzerg-perl Recommends: librg-reprof-bundle-perl -Suggests: python-corepywrap -Comment: py2removal +Recommends: python3-corepywrap Recommends: librcsb-core-wrapper0-dev @@ -140,10 +138,6 @@ Suggests: r-bioc-affy, r-bioc-multiassayexperiment, r-bioc-nanostringqcpro, r-bioc-org.hs.eg.db, - r-bioc-org.mm.eg.db, - r-bioc-org.dm.eg.db, - r-bioc-org.rn.eg.db, - r-bioc-org.ce.eg.db r-bioc-pcamethods, r-bioc-phyloseq, r-bioc-preprocesscore, @@ -249,7 +243,7 @@ Recommends: r-cran-samr Recommends: r-cran-sctransform Recommends: r-cran-seurat -https://salsa.debian.org/blends-team/med/-/graphs/master + Recommends: r-cran-seqinr Suggests: r-cran-shazam @@ -374,8 +368,7 @@ Recommends: libgff-dev Recommends: python3-pysam -Suggests: python-pbcore -Comment: py2removal +Recommends: python3-pbcore Recommends: python3-cobra @@ -395,8 +388,7 @@ Recommends: python3-pbconsensuscore Recommends: python3-consensuscore2, libconsensuscore-dev -Suggests: python-pbcommand -Comment: py2removal +Recommends: python3-pbcommand Recommends: python3-pyvcf @@ -404,8 +396,7 @@ Recommends: python3-pyfaidx Recommends: python3-sqt -Suggests: python-kineticstools -Comment: py2removal +Recommends: python3-kineticstools Suggests: libbam-dev @@ -472,7 +463,7 @@ Recommends: python3-gffutils Recommends: python3-bx -Recommends: toil, galaxy-lib +Recommends: toil, python3-galaxy-lib Suggets: cthreadpool-dev @@ -540,7 +531,7 @@ Recommends: python3-deeptools, python3-deeptoolsintervals, python3-py2bit Recommends: python3-loompy -Recommends: gffread, libgclib +Recommends: gffread, libgclib-dev Ignore: golang-github-biogo-hts-dev Comment: As explained on the Debian Med mailing list ===================================== tasks/cloud ===================================== @@ -62,8 +62,8 @@ Comment: Oligonucleotides and PCR Recommends: acedb-other, disulfinder, ncbi-tools-bin, ncoils, readseq, tigr-glimmer, seqan-apps, staden-io-lib-utils -Suggests: python-cogent -Comment: py2removal +Recommends: python3-cogent3 + X-End-Category: Tools for the molecular biologist. X-Begin-Category: Others View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/69f1c951d5a4ab4a2077f007350b7c7eafb5a408 -- View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/69f1c951d5a4ab4a2077f007350b7c7eafb5a408 You're receiving this email because of your account on salsa.debian.org.
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