[Blends-commit] [Git][blends-team/med][master] 2 commits: zalign removed from Debian

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
b34b6708 by Andreas Tille at 2022-08-14T21:18:24+02:00
zalign removed from Debian

- - - - -
57c82abd by Andreas Tille at 2022-10-10T13:39:46+02:00
Update list of packages maintained by Debian Med team

- - - - -


7 changed files:

- debian/changelog
- tasks/bio
- tasks/bio-dev
- tasks/cloud
- tasks/imaging
- tasks/imaging-dev
- tasks/psychology


Changes:

=====================================
debian/changelog
=====================================
@@ -3,6 +3,7 @@ debian-med (3.7.3) UNRELEASED; urgency=medium
   * Build-Depends-Indep: blends-dev (>= 0.7.5~)
     Closes: #1012341
   * dicompyler removed from Debian thus from oncology task
+  * zalign removed from Debian
 
  -- Andreas Tille <tille at debian.org>  Fri, 03 Jun 2022 12:06:56 +0200
 


=====================================
tasks/bio
=====================================
@@ -484,6 +484,8 @@ Recommends: gasic
 
 Recommends: ipig
 
+Recommends: abpoa
+
 Recommends: aevol
 
 Recommends: agat
@@ -678,6 +680,8 @@ Recommends: fastml
 
 Recommends: fastp
 
+Recommends: fastq-pair
+
 Recommends: fastqc
 
 Recommends: fastqtl
@@ -732,6 +736,8 @@ Recommends: genomethreader
 
 Recommends: genometools
 
+Recommends: genomicsdb-tools
+
 Recommends: gerp++
 
 Recommends: gffread
@@ -885,7 +891,7 @@ Recommends: meryl
 
 Recommends: metabit
 
-Recommends: metaphlan2
+Recommends: metaphlan
 
 Recommends: metastudent
 
@@ -970,6 +976,8 @@ Recommends: ntcard
 
 Recommends: nw-align
 
+Recommends: nxtrim
+
 Recommends: oases
 
 Recommends: obitools
@@ -1105,8 +1113,12 @@ Recommends: pssh2
 
 Recommends: pufferfish
 
+Recommends: pullseq
+
 Recommends: pycorrfit
 
+Recommends: pyensembl
+
 Recommends: pyscanfcs
 
 Suggests: python3-alignlib
@@ -1464,6 +1476,8 @@ Recommends: situs
 
 Recommends: sim4db
 
+Recommends: ska
+
 Recommends: skesa
 
 Recommends: smalt
@@ -1531,6 +1545,8 @@ Recommends: sumtrees
 
 Recommends: surankco
 
+Recommends: surpyvor
+
 Recommends: survivor
 
 Recommends: svim
@@ -1543,6 +1559,8 @@ X-Importance: powerful
 
 Recommends: tantan
 
+Recommends: terraphast
+
 Recommends: thesias
 
 Recommends: tiddit
@@ -1593,6 +1611,8 @@ Recommends: uncalled
 
 Recommends: unicycler
 
+Recommends: unikmer
+
 Recommends: varna
 
 Recommends: varmatch
@@ -1618,6 +1638,8 @@ Recommends: vsearch
 
 Recommends: vt
 
+Recommends: xpore
+
 Recommends: yaha
 
 Recommends: yanagiba
@@ -1627,8 +1649,6 @@ Recommends: yanosim
 Recommends: canu
 Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Recommends: zalign
-
 Recommends: zodiac-zeden
 Language: C, C++
 


=====================================
tasks/bio-dev
=====================================
@@ -40,7 +40,7 @@ Recommends: python3-tinyalign
 
 Recommends: ruby-bio
 
-Recommends: libbiojava-java, libbiojava4-java
+Recommends: libbiojava-java, libbiojava4-java, libbiojava5-java
 
 Recommends: libgenome-dev, libmuscle-dev, libmems-dev
 
@@ -105,6 +105,8 @@ Recommends: libpdb-redo-dev
 
 Recommends: libbioparser-dev, libspoa-dev, libedlib-dev, libthread-pool-dev
 
+Recommends: python3-pyspoa
+
 Recommends: libjebl2-java
 Remark: Fork from jebl
  This is a branch of the original JEBL on
@@ -474,6 +476,8 @@ Suggests: libfast-perl
 
 Recommends: libfast5-dev, python3-fast5
 
+Recommends: ont-fast5-api
+
 Recommends: libpbseq-dev, libpbdata-dev, libpbihdf-dev, libblasr-dev
 
 Suggests: libpbcopper-dev
@@ -614,6 +618,8 @@ Recommends: libhtscodecs-dev
 
 Recommends: python3-torch
 
+Recommends: python3-pyabpoa
+
 Recommends: python3-anndata
 
 Recommends: python3-bx
@@ -644,7 +650,27 @@ Suggests: libsuma-dev
 
 Recommends: python3-scanpy
 
+Recommends: python3-propka
+
 Recommends: python3-cigar
 
 Recommends: python3-compclust
 X-Category: Genomics; Clustering analysis (+GUI)
+
+Suggests: capsule-nextflow, libcapsule-maven-nextflow-java
+
+Suggests: libgatk-bwamem-java, libgatk-bwamem-jni, libgatk-fermilite-java, libgatk-fermilite-jni, libgenomicsdb-java, libgenomicsdb-dev
+
+Suggests: libicb-utils-java
+
+Suggests: libbiosoup-dev
+
+Recommends: libslow5-dev, python3-slow5
+
+Suggests: libvbz-hdf-plugin-dev
+
+Suggests: python3-bioblend
+
+Recommends: python3-gtfparse
+
+Suggests: libterraces-dev


=====================================
tasks/cloud
=====================================
@@ -22,7 +22,7 @@ Recommends: amap-align, blast2, biosquid, boxshade, cassiopee, cdbfasta,
             embassy-phylip, exonerate, gff2aplot, gff2ps, glam2, gmap, hmmer,
             jellyfish, kalign, mafft, mlv-smile, mummer, muscle, neobio, poa,
             prank, probcons, proda, sibsim4, sigma-align, sim4, snap,
-            squizz, t-coffee, wise, zalign
+            squizz, t-coffee, wise
 X-End-Category: Sequence alignments and related programs.
 
 X-Begin-Category: High throughput sequencing


=====================================
tasks/imaging
=====================================
@@ -19,6 +19,8 @@ Suggests: illustrate
 
 Recommends: nifti-bin
 
+Recommends: heudiconv
+
 Recommends: aeskulap
 
 Recommends: fsl
@@ -97,7 +99,7 @@ Recommends: crea
 
 Recommends: orthanc
 
-Suggests: orthanc-webviewer, orthanc-dicomweb, orthanc-imagej, orthanc-postgresql, orthanc-mysql, orthanc-gdcm
+Suggests: orthanc-webviewer, orthanc-dicomweb, orthanc-imagej, orthanc-postgresql, orthanc-mysql, orthanc-gdcm, orthanc-neuro
 
 Recommends: teem-apps
 


=====================================
tasks/imaging-dev
=====================================
@@ -20,6 +20,8 @@ Recommends: libgdcm2-dev
 
 Recommends: python3-gdcm
 
+Recommends: python3-dcmstack
+
 Suggests: libics-dev
 
 Recommends: libmaxflow-dev


=====================================
tasks/psychology
=====================================
@@ -33,5 +33,7 @@ Recommends: r-cran-psychotree
 
 Recommends: r-cran-psyphy
 
+Recommends: orthanc-neuro
+
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Psychometrics.html



View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/5c1c7d45c2f873d80048d103063585fab64391e9...57c82abd412b6e7c7894912a0465f10e55419b58

-- 
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/5c1c7d45c2f873d80048d103063585fab64391e9...57c82abd412b6e7c7894912a0465f10e55419b58
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