[Blends-commit] [Git][blends-team/med][master] Cleanup tasks: Some packages are ported to Python3, some were just wrongly spelled, syntax fixes

[Andreas Tille]

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

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