[med-svn] [Git][med-team/bcbio][master] Always use our Rscript.
Steffen Möller pushed to branch master at Debian Med / bcbio
Commits:
ffdc3278 by Steffen Moeller at 2021-05-07T23:55:11+02:00
Always use our Rscript.
- - - - -
5 changed files:
- debian/README.source
- debian/changelog
- debian/control
- + debian/patches/RscriptIsSystemVersion.patch
- debian/patches/series
Changes:
=
debian/README.source
=
@@ -4,5 +4,9 @@ bcbio for Debian
Please be aware that this package provides what upstream distributes
as bcbio-nextgen.
+debian/patches/RscriptIsSystemVersion.patch:
+ This Debian package should always work with Debian's Rscript since
+ we have also installed our R modules with the system.
+
-- Steffen Moeller Sun, 11 Feb 2018 18:40:28 +0100
=
debian/changelog
=
@@ -4,6 +4,7 @@ bcbio (1.2.8-1) UNRELEASED; urgency=medium
* Standards-Version: 4.5.1 (routine-update)
* Removed now obsolete patch on abc collections
* Updated dependencies
+ * Point to system version of Rscript - always
-- Steffen Moeller Fri, 07 May 2021 20:29:57 +0200
=
debian/control
=
@@ -56,13 +56,15 @@ Build-Depends: debhelper-compat (= 13),
pythonpy ,
rapmap ,
rna-star ,
- r-other-wasabi ,
+ r-base-core ,
r-bioc-htsfilter ,
r-bioc-degreport ,
r-bioc-purecn ,
+ r-bioc-summarizedexperiment ,
r-cran-tidyverse ,
r-bioc-titancna ,
r-bioc-tximport ,
+ r-other-wasabi ,
salmon ,
samblaster ,
samtools ,
@@ -182,6 +184,8 @@ Suggests: toil,
tophat2,
# found in source code but not exactly sure about its importance
tophat-recondition,
+ r-bioc-summarizedexperiment,
+ r-cran-tidyverse,
r-other-wasabi
Description: toolkit for analysing high-throughput sequencing data
This package installs the command line tools of the bcbio-nextgen
=
debian/patches/RscriptIsSystemVersion.patch
=
@@ -0,0 +1,33 @@
+Author: Steffen Moeller
+Description: With Debian we want to use _our_ R installation, while with the
+ typical conda-installation of bcbio this is the other way around. It is
+ important not to mix these up, hence this strict return of the sytem
+ version.
+ This patch is not meant to be sent upstream.
+
+Index: bcbio/bcbio/utils.py
+===
+--- bcbio.orig/bcbio/utils.py
bcbio/bcbio/utils.py
+@@ -694,18 +694,11 @@ def dictapply(d, fn):
+ return d
+
+ def Rscript_cmd(env="base"):
+-"""Retrieve path to locally installed Rscript in the given env.
++"""Original bcbio: Retrieve path to locally installed Rscript in the
given env.
+ Prefers Rscript version installed via conda to a system version.
++Debian: We use ours.
+ """
+-if env == "base":
+-rscript = which(os.path.join(get_bcbio_bin(), "Rscript"))
+-else:
+-conda_dir = get_conda_dir()
+-rscript = os.path.join(conda_dir, "envs", env, "bin", "Rscript")
+-if rscript:
+-return rscript
+-else:
+-return which("Rscript")
++return "/usr/bin/Rscript"
+
+ def R_sitelib(env="base"):
+ """Retrieve the R site-library installed with the bcbio installer for a
given
=
debian/patches/series
=
@@ -6,3 +6,4 @@ pythonpaths.patch
hts_nim_tools.patch
cnvkitPath.patch
fixeFreetypePreload.patch
+RscriptIsSystemVersion.patch
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7
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[med-svn] [Git][med-team/bcbio] Pushed new tag upstream/1.2.5
Steffen Möller pushed new tag upstream/1.2.5 at Debian Med / bcbio -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/tree/upstream/1.2.5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio] Pushed new tag upstream/1.2.8
Steffen Möller pushed new tag upstream/1.2.8 at Debian Med / bcbio -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/tree/upstream/1.2.8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][master] 5 commits: New upstream version 1.2.8
Steffen Möller pushed to branch master at Debian Med / bcbio Commits: 6d1de787 by Steffen Moeller at 2021-05-07T20:29:57+02:00 New upstream version 1.2.8 - - - - - c2d9ba19 by Steffen Moeller at 2021-05-07T20:29:57+02:00 routine-update: New upstream version - - - - - 5e993c9a by Steffen Moeller at 2021-05-07T20:30:42+02:00 Update upstream source from tag upstream/1.2.8 Update to upstream version 1.2.8 with Debian dir 6a59ce8b07eb9a17d3fb1fc1a8dfe3cf437b3159 - - - - - c3259f06 by Steffen Moeller at 2021-05-07T20:30:42+02:00 routine-update: Standards-Version: 4.5.1 - - - - - cd8feac3 by Steffen Moeller at 2021-05-07T20:42:27+02:00 routine-update: Restructuring of d/control - - - - - 30 changed files: - HISTORY.md - LICENSE.txt - bcbio/chipseq/atac.py - bcbio/chipseq/macs2.py - bcbio/chipseq/peaks.py - bcbio/ngsalign/bismark.py - bcbio/ngsalign/bwa.py - bcbio/pipeline/qcsummary.py - bcbio/pipeline/rnaseq.py - bcbio/pipeline/run_info.py - bcbio/qc/contamination.py - bcbio/qc/multiqc.py - bcbio/qc/qualimap.py - bcbio/rnaseq/gtf.py - bcbio/structural/purecn.py - bcbio/structural/regions.py - bcbio/structural/titancna.py - bcbio/upload/__init__.py - bcbio/variation/gatkjoint.py - bcbio/variation/mutect2.py - bcbio/wgbsseq/align.py - bcbio/wgbsseq/deduplication.py - bcbio/wgbsseq/kits.py - bcbio/workflow/template.py - config/examples/cancer-dream-syn3.yaml - + config/templates/purecn_pon.yaml - config/templates/somatic-duplex-umi.yaml - debian/changelog - debian/control - docs/conf.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/68261fcdb35b8f5d078023944114bc5b465cb884...cd8feac301800694e286f39f4104597b70d1d857 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/68261fcdb35b8f5d078023944114bc5b465cb884...cd8feac301800694e286f39f4104597b70d1d857 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/vsearch][master] Update metadata - added guix, fixed indent
Steffen Möller pushed to branch master at Debian Med / vsearch Commits: 87aafc8e by Steffen Möller at 2021-04-14T12:06:04+00:00 Update metadata - added guix, fixed indent - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,25 +1,27 @@ Bug-Database: https://github.com/torognes/vsearch/issues Bug-Submit: https://github.com/torognes/vsearch/issues/new Reference: -- Author: > + - Author: > Torbjørn Rognes and Tomáš Flouri and Ben Nichols and Christopher Quince and Frédéric Mahé - Journal: PeerJ - Title: > + Journal: PeerJ + Title: > VSEARCH: a versatile open source tool for metagenomics - URL: https://peerj.com/articles/2584/ - ePrint: https://peerj.com/articles/2584.pdf - Volume: 4 - Pages: e2584 - DOI: 10.7717/peerj.2584 + URL: https://peerj.com/articles/2584/ + ePrint: https://peerj.com/articles/2584.pdf + Volume: 4 + Pages: e2584 + DOI: 10.7717/peerj.2584 Registry: -- Name: OMICtools - Entry: OMICS_14601 -- Name: bio.tools - Entry: vsearch -- Name: SciCrunch - Entry: NA -- Name: conda:bioconda - Entry: vsearch + - Name: OMICtools + Entry: OMICS_14601 + - Name: bio.tools + Entry: vsearch + - Name: SciCrunch + Entry: NA + - Name: conda:bioconda + Entry: vsearch + - Name: guix + Entry: vsearch Repository: https://github.com/torognes/vsearch.git Repository-Browse: https://github.com/torognes/vsearch View it on GitLab: https://salsa.debian.org/med-team/vsearch/-/commit/87aafc8e9fce863b18df0eb6ace9584d0d947be4 -- View it on GitLab: https://salsa.debian.org/med-team/vsearch/-/commit/87aafc8e9fce863b18df0eb6ace9584d0d947be4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/nxtrim][master] Update metadata - added ref to registries
Steffen Möller pushed to branch master at Debian Med / nxtrim Commits: d785766f by Steffen Möller at 2021-04-05T17:28:23+00:00 Update metadata - added ref to registries - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -5,3 +5,11 @@ Bug-Submit: https://github.com/sequencing/NxTrim/issues/new Changelog: https://github.com/sequencing/NxTrim/tags Repository: https://github.com/sequencing/NxTrim.git Repository-Browse: https://github.com/sequencing/NxTrim +Registry: + - Name: bio.tools + Entry: nxtrim + - Name: conda:bioconda + Entry: nxtrim + - Name: guix + Entry: NA + Checked: 2021-04-05 View it on GitLab: https://salsa.debian.org/med-team/nxtrim/-/commit/d785766fd1a7a71ae7fda066c3547ce16b034b7d -- View it on GitLab: https://salsa.debian.org/med-team/nxtrim/-/commit/d785766fd1a7a71ae7fda066c3547ce16b034b7d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/snpeff][master] Update control - improved wording.
Steffen Möller pushed to branch master at Debian Med / snpeff
Commits:
e67d7d5d by Steffen Möller at 2021-03-30T17:44:04+00:00
Update control - improved wording.
- - - - -
1 changed file:
- debian/control
Changes:
=
debian/control
=
@@ -68,12 +68,13 @@ Depends: ${java:Depends},
libsnpeff-java (= ${binary:Version})
Suggests: vcfanno
Description: genetic variant annotation and effect prediction toolbox - tool
- "We are all different!" Geneticists agree to this old Monty Python joke..
+ "We are all different!" Geneticists agree to this.
Even twins, who are said to be identical are on a molecular
level only "mostly" identical. And even within the exact same individual,
healthy cells acquire mutations such that we are all genetic mosaics.
- This happens upon environmental factors, e.g. like UV light, but also
- as random mishaps during cellular divisions.
+ Changes to individual cells may be induced by environmental factors,
+ e.g. like UV light, or happen sporadically as mishaps during cellular
+ divisions.
.
Because there are so many genetic differences, and most have just no
particular meaning for the development of a phenotype, i.e. most have no
View it on GitLab:
https://salsa.debian.org/med-team/snpeff/-/commit/e67d7d5dd691a49d1fc66055a4ddb155bf25ed24
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[med-svn] [Git][med-team/snpeff][master] Update control - extended description
Steffen Möller pushed to branch master at Debian Med / snpeff
Commits:
0b6a8a87 by Steffen Möller at 2021-03-30T16:01:25+00:00
Update control - extended description
- - - - -
1 changed file:
- debian/control
Changes:
=
debian/control
=
@@ -66,11 +66,29 @@ Architecture: all
Depends: ${java:Depends},
${misc:Depends},
libsnpeff-java (= ${binary:Version})
+Suggests: vcfanno
Description: genetic variant annotation and effect prediction toolbox - tool
+ "We are all different!" Geneticists agree to this old Monty Python joke..
+ Even twins, who are said to be identical are on a molecular
+ level only "mostly" identical. And even within the exact same individual,
+ healthy cells acquire mutations such that we are all genetic mosaics.
+ This happens upon environmental factors, e.g. like UV light, but also
+ as random mishaps during cellular divisions.
+ .
+ Because there are so many genetic differences, and most have just no
+ particular meaning for the development of a phenotype, i.e. most have no
+ effect, it would be nice to have heuristics implemented that direct the
+ researcher towards single-nucleotide polymorphisms (SNPs) that are most
+ likely to be relevant. This identifies the gene that causes or contributes
+ to, e.g, an illness, and possibly also genes that are affected by that
+ change. Such mechanistic understanding of a disease, particularly when
+ multiple genes and multiple genetic variants are contributing to the
+ then "polgygenic" phenotype, is at the onset of drug development and
+ increasingly also for selecting individualize therapies in the clinic.
+ .
SnpEff is a variant annotation and effect prediction tool. It annotates
and predicts the effects of variants on genes (such as amino acid
changes).
- .
The inputs are predicted variants (SNPs, insertions, deletions and
MNPs). The input file is usually obtained as a result of a sequencing
experiment, and it is usually in variant call format (VCF).
View it on GitLab:
https://salsa.debian.org/med-team/snpeff/-/commit/0b6a8a8782a44c45d3f70339102b2e67130ef3e4
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[med-svn] [Git][med-team/snpeff][master] Update metadata - added refs to guix+SciCrunch
Steffen Möller pushed to branch master at Debian Med / snpeff Commits: 508aa876 by Steffen Möller at 2021-03-30T14:35:39+00:00 Update metadata - added refs to guix+SciCrunch - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -25,5 +25,10 @@ Registry: Entry: snpeff - Name: conda:bioconda Entry: snpeff + - Name: guix + Entry: NA + Checked: 2021-03-30 + - Name: SciCrunch + Entry: SCR_005191 Repository: https://github.com/pcingola/SnpEff.git Repository-Browse: https://github.com/pcingola/SnpEff View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/508aa8761b1e00e4eecdae86063c04fae34ca0fe -- View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/508aa8761b1e00e4eecdae86063c04fae34ca0fe You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pangolearn][master] d/u/metadata - registry
Steffen Möller pushed to branch master at Debian Med / python-pangolearn Commits: 3bc14609 by Steffen Möller at 2021-03-28T14:25:11+00:00 d/u/metadata - registry - - - - - 1 changed file: - + debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -0,0 +1,9 @@ +Registry: + - Name: guix + Entry: NA + Checked: 2021-03-28 + - Name: conda:bioconda + Entry: pangolearn + - Name: bio.tools + Entry: NA + Checked: 2021-03-28 View it on GitLab: https://salsa.debian.org/med-team/python-pangolearn/-/commit/3bc146098bf3575d931b135524ca7ca57f8f3660 -- View it on GitLab: https://salsa.debian.org/med-team/python-pangolearn/-/commit/3bc146098bf3575d931b135524ca7ca57f8f3660 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pangolearn][master] Update control - found mafft mentioned in a description
Steffen Möller pushed to branch master at Debian Med / python-pangolearn
Commits:
f1af633d by Steffen Möller at 2021-03-28T14:19:22+00:00
Update control - found mafft mentioned in a description
- - - - -
1 changed file:
- debian/control
Changes:
=
debian/control
=
@@ -17,6 +17,7 @@ Package: python3-pangolearn
Architecture: all
Section: python
Depends: ${python3:Depends}, ${misc:Depends}
+Suggests: mafft
Description: store of the trained model for pangolin to access
Pangolin runs a multinomial logistic regression model trained against
lineage assignments based on GISAID data.
View it on GitLab:
https://salsa.debian.org/med-team/python-pangolearn/-/commit/f1af633d7ff1f1c5b135cc5ce3bf1b25cd174f2b
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[med-svn] [Git][med-team/bbmap][master] Added d/u/metadata
Steffen Möller pushed to branch master at Debian Med / bbmap Commits: 7a0b4b6a by Steffen Möller at 2021-03-25T20:57:36+00:00 Added d/u/metadata - - - - - 1 changed file: - + debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -0,0 +1,27 @@ +Reference: + - Name: > +Brian Bushnell and Jonathan Rood and Esther Singer + Title: > +BBMerge – Accurate paired shotgun read merging via overlap + Journal: PLOS One + Month: Oct + Day: 26 + Year: 2017 + URL: https://doi.org/10.1371/journal.pone.0185056 + DOI: 10.1371/journal.pone.0185056 + PMID: 29073143 + ePrint: "https://journals.plos.org/plosone/article/file?id=\ +10.1371/journal.pone.0185056=printable" +Registry: + - Name: bio.tools + Entry: bbmap + - Name: conda:bioconda + Entry: bbmap + - Name: guix + Entry: bbmap + - Name: SciCrunch + Entry: SCR_016968 + Comment: for bbtools + - Name: SciCrunch + Entry: SCR_016965 + Comment: for bbmap View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/commit/7a0b4b6a1b15d2a420fb784adbe8c452af7d0292 -- View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/commit/7a0b4b6a1b15d2a420fb784adbe8c452af7d0292 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bbmap][master] Update control - explained equivalence with BBTools
Steffen Möller pushed to branch master at Debian Med / bbmap
Commits:
59d349c9 by Steffen Möller at 2021-03-25T20:17:56+00:00
Update control - explained equivalence with BBTools
- - - - -
1 changed file:
- debian/control
Changes:
=
debian/control
=
@@ -18,16 +18,20 @@ Package: bbmap
Architecture: all
Depends: ${java:Depends},
${misc:Depends}
+Provides: bbtools
Recommends: pigz
-Description: short read aligner and other bioinformatic tools
+Description: BBTools genomic aligner and other tools for short sequences
+ The BBTools are a collection of of small programs to solve recurrent
+ tasks for the creative handling of short biological RNA/DNA sequences.
+ This suite may be best known for its mapper, which is also the name of
+ the project on sourceforge, but several tools have been added over time..
+ All tools are multi-threaded, implemented platform-independently in Java:
+ .
BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling
arbitrarily large genomes with millions of scaffolds. Handles Illumina,
PacBio, 454, and other reads; very high sensitivity and tolerant of
errors and numerous large indels.
.
- BBMap is multithreaded as well as the other tools bundled into this
- package for instance:
- .
BBNorm: Kmer-based error-correction and normalization tool.
.
Dedupe: Simplifies assemblies by removing duplicate or contained
View it on GitLab:
https://salsa.debian.org/med-team/bbmap/-/commit/59d349c919b7b98cd753fe4ca998f18aef855094
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[med-svn] [Git][med-team/scanpy][master] Update metadata - added paper and registry entries
Steffen Möller pushed to branch master at Debian Med / scanpy Commits: 78277c0c by Steffen Möller at 2021-03-23T21:39:24+00:00 Update metadata - added paper and registry entries - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -5,3 +5,26 @@ Bug-Submit: https://github.com/theislab/scanpy/issues/new Changelog: https://github.com/theislab/scanpy/tags Repository: https://github.com/theislab/scanpy.git Repository-Browse: https://github.com/theislab/scanpy +Reference: + - Author: > +F. Alexander Wolf and Philipp Angerer and Fabian J. Theis + Title: > +SCANPY: large-scale single-cell gene expression data analysis + Journal: Genome Biology + Volume 19 + Number: 15 + Year: 2018 + URL: "https://genomebiology.biomedcentral.com/articles/\ +10.1186/s13059-017-1382-0" + DOI: 10.1186/s13059-017-1382-0 + ePrint: "https://genomebiology.biomedcentral.com/track/pdf/\ +10.1186/s13059-017-1382-0.pdf" +Registry: + - Name: bio.tools + Entry: scanpy + - Name: conda:bioconda + Entry: scanpy + - Name: SciCrunch + Entry: SCR_018139 + - Name: guix + Entry: python-scanpy View it on GitLab: https://salsa.debian.org/med-team/scanpy/-/commit/78277c0c77258cedb6625159702603e0d3b5f6be -- View it on GitLab: https://salsa.debian.org/med-team/scanpy/-/commit/78277c0c77258cedb6625159702603e0d3b5f6be You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bwa][master] Update metadata - ref to guix
Steffen Möller pushed to branch master at Debian Med / bwa Commits: ad2853f2 by Steffen Möller at 2021-03-06T23:16:05+00:00 Update metadata - ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -26,3 +26,5 @@ Registry: Entry: OMICS_00654 - Name: conda:bioconda Entry: bwa + - Name: guix + Entry: bwa View it on GitLab: https://salsa.debian.org/med-team/bwa/-/commit/ad2853f2bf56d131b480034ac5e4f5e5646f0920 -- View it on GitLab: https://salsa.debian.org/med-team/bwa/-/commit/ad2853f2bf56d131b480034ac5e4f5e5646f0920 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/blasr][master] Update metadata - indent, ref to guix
Steffen Möller pushed to branch master at Debian Med / blasr Commits: 4c589b7e by Steffen Möller at 2021-03-06T23:14:28+00:00 Update metadata - indent, ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,21 +1,23 @@ Reference: - Author: Mark J Chaisson and Glenn Tesler - Title: > - Mapping single molecule sequencing reads using basic local alignment - with successive refinement (BLASR): application and theory - Journal: BMC Bioinformatics - Year: 2012 - Volume: 13 - Number: 238 - DOI: 10.1186/1471-2105-13-23 - PMID: 22988817 - URL: http://www.biomedcentral.com/1471-2105/13/238 + - Author: Mark J Chaisson and Glenn Tesler + Title: > +Mapping single molecule sequencing reads using basic local alignment +with successive refinement (BLASR): application and theory + Journal: BMC Bioinformatics + Year: 2012 + Volume: 13 + Number: 238 + DOI: 10.1186/1471-2105-13-23 + PMID: 22988817 + URL: http://www.biomedcentral.com/1471-2105/13/238 Registry: - - Name: OMICtools -Entry: OMICS_05134 - - Name: SciCrunch -Entry: SCR_000764 - - Name: bio.tools -Entry: Blasr - - Name: conda:bioconda -Entry: blasr + - Name: OMICtools + Entry: OMICS_05134 + - Name: SciCrunch + Entry: SCR_000764 + - Name: bio.tools + Entry: Blasr + - Name: conda:bioconda + Entry: blasr + - Name: guix + Entry: blasr View it on GitLab: https://salsa.debian.org/med-team/blasr/-/commit/4c589b7ececd465b94f63ec752897894ee6c483f -- View it on GitLab: https://salsa.debian.org/med-team/blasr/-/commit/4c589b7ececd465b94f63ec752897894ee6c483f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bedtools][master] Update metadata - indent, added ref to guix
Steffen Möller pushed to branch master at Debian Med / bedtools Commits: 305fa2ad by Steffen Möller at 2021-03-06T23:12:27+00:00 Update metadata - indent, added ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -2,27 +2,29 @@ Archive: GitHub Bug-Database: https://github.com/arq5x/bedtools2/issues Bug-Submit: https://github.com/arq5x/bedtools2/issues/new Reference: - Author: Quinlan, Aaron R. and Hall, Ira M. - Title: > + - Author: Quinlan, Aaron R. and Hall, Ira M. + Title: > BEDTools: a flexible suite of utilities for comparing genomic features - Volume: 26 - Number: 6 - Pages: 841-842 - Year: 2010 - DOI: 10.1093/bioinformatics/btq033 - URL: http://bioinformatics.oxfordjournals.org/content/26/6/841.abstract - ePrint: > + Volume: 26 + Number: 6 + Pages: 841-842 + Year: 2010 + DOI: 10.1093/bioinformatics/btq033 + URL: http://bioinformatics.oxfordjournals.org/content/26/6/841.abstract + ePrint: > http://bioinformatics.oxfordjournals.org/content/26/6/841.full.pdf+html - Journal: Bioinformatics - PMID: 20110278 + Journal: Bioinformatics + PMID: 20110278 Repository: https://github.com/arq5x/bedtools2.git Repository-Browse: https://github.com/arq5x/bedtools2 Registry: -- Name: SciCrunch - Entry: SCR_006646 -- Name: bio.tools - Entry: bedtools -- Name: OMICtools - Entry: OMICS_01159 -- Name: conda:bioconda - Entry: biotools + - Name: SciCrunch + Entry: SCR_006646 + - Name: bio.tools + Entry: bedtools + - Name: OMICtools + Entry: OMICS_01159 + - Name: conda:bioconda + Entry: biotools + - Name: guix + Entry: bedtools View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/commit/305fa2adcb9cbdecff2f7437bbeee258a2091168 -- View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/commit/305fa2adcb9cbdecff2f7437bbeee258a2091168 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bedops][master] Update metadata - indent plus ref to guix
Steffen Möller pushed to branch master at Debian Med / bedops Commits: 8bf607b7 by Steffen Möller at 2021-03-06T23:10:16+00:00 Update metadata - indent plus ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,31 +1,35 @@ Cite-As: | - Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al. - BEDOPS: high-performance genomic feature operations - Bioinformatics (2012) 28 (14): 1919-1920. + Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al. + BEDOPS: high-performance genomic feature operations + Bioinformatics (2012) 28 (14): 1919-1920. Reference: -- Author: > + - Author: > Shane Neph and M. Scott Kuehn and Alex P. Reynolds and Eric Haugen and Robert E. Thurman and Audra K. Johnson and Eric Rynes and Matthew T. Maurano and Jeff Vierstra and Sean Thomas and Richard Sandstrom and Richard Humbert and John A. Stamatoyannopoulos - Title: 'BEDOPS: high-performance genomic feature operations' - Publisher: Bioinformatics - Year: 2012 - Volume: 28 - Number: 14 - Pages: 1919-1920 - DOI: 10.1093/bioinformatics/bts277 - PMID: 22576172 - URL: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract - eprint: https://academic.oup.com/bioinformatics/article-pdf/28/14/1919/582641/bts277.pdf + Title: > +BEDOPS: high-performance genomic feature operations + Publisher: Bioinformatics + Year: 2012 + Volume: 28 + Number: 14 + Pages: 1919-1920 + DOI: 10.1093/bioinformatics/bts277 + PMID: 22576172 + URL: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract + eprint: "https://academic.oup.com/bioinformatics/article-pdf/\ +28/14/1919/582641/bts277.pdf" Registry: -- Name: bio.tools - Entry: Bedops -- Name: OMICtools - Entry: OMICS_00949 -- Name: SciCrunch - Entry: SCR_012865 -- Name: conda:bioconda - Entry: bedops + - Name: bio.tools + Entry: Bedops + - Name: OMICtools + Entry: OMICS_00949 + - Name: SciCrunch + Entry: SCR_012865 + - Name: conda:bioconda + Entry: bedops + - Name: guix + Entry: bedops Bug-Database: https://github.com/bedops/bedops/issues Bug-Submit: https://github.com/bedops/bedops/issues/new View it on GitLab: https://salsa.debian.org/med-team/bedops/-/commit/8bf607b74082830e71f0a68c26c5fd9097814000 -- View it on GitLab: https://salsa.debian.org/med-team/bedops/-/commit/8bf607b74082830e71f0a68c26c5fd9097814000 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcftools][master] Update metadata - added ref to guix
Steffen Möller pushed to branch master at Debian Med / bcftools Commits: 4d41ed57 by Steffen Möller at 2021-03-06T23:08:06+00:00 Update metadata - added ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -17,5 +17,7 @@ Registry: Entry: bcftools - Name: conda:bioconda Entry: bcftools + - Name: guix + Entry: bcftools Repository: https://github.com/samtools/bcftools.git Repository-Browse: https://github.com/samtools/bcftools View it on GitLab: https://salsa.debian.org/med-team/bcftools/-/commit/4d41ed5751b43a9370dc6fbc6d80a5b8cddeafed -- View it on GitLab: https://salsa.debian.org/med-team/bcftools/-/commit/4d41ed5751b43a9370dc6fbc6d80a5b8cddeafed You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bioawk][master] Update metadata - added references to registries
Steffen Möller pushed to branch master at Debian Med / bioawk Commits: c7000a2b by Steffen Möller at 2021-03-06T23:06:53+00:00 Update metadata - added references to registries - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -5,3 +5,11 @@ Bug-Submit: https://github.com/lh3/bioawk/issues/new Changelog: https://github.com/lh3/bioawk/tags Repository: https://github.com/lh3/bioawk.git Repository-Browse: https://github.com/lh3/bioawk +Registry: + - Name: guix + Entry: bioawk + - Name: conda:bioconda + Entry: bioawk + - Name: bio.tools + Entry: NA + Checked: 2021-03-06 View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/commit/c7000a2bc919120665729f307a5698b9e79008b1 -- View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/commit/c7000a2bc919120665729f307a5698b9e79008b1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bowtie][master] Update metadata - fixed yaml, fixed indent, added guix
Steffen Möller pushed to branch master at Debian Med / bowtie Commits: 344c83aa by Steffen Möller at 2021-03-06T23:02:05+00:00 Update metadata - fixed yaml, fixed indent, added guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,24 +1,28 @@ Bug-Database: https://github.com/BenLangmead/bowtie/issues Bug-Submit: https://github.com/BenLangmead/bowtie/issues/new Reference: - author: "Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg\n" - title: "Ultrafast and memory-efficient alignment of short DNA sequences to the human\ -\ genome\n" - journal: Genome Biology - volume: 10 - pages: R25 - year: 2009 - DOI: 10.1186/gb-2009-10-3-r25 - URL: http://genomebiology.com/2009/10/3/R25 - eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf + - Author: > +Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg + Title: > +Ultrafast and memory-efficient alignment of short DNA sequences to the +human genome + Journal: Genome Biology + Volume: 10 + Pages: R25 + Year: 2009 + DOI: 10.1186/gb-2009-10-3-r25 + URL: http://genomebiology.com/2009/10/3/R25 + eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf Registry: -- Name: SciCrunch - Entry: SCR_005476 -- Name: OMICtools - Entry: OMICS_00653 -- Name: bio.tools - Entry: bowtie -- Name: conda:bioconda - Entry: bowtie + - Name: SciCrunch + Entry: SCR_005476 + - Name: OMICtools + Entry: OMICS_00653 + - Name: bio.tools + Entry: bowtie + - Name: conda:bioconda + Entry: bowtie + - Name: guix + Entry: bowtie1 Repository: https://github.com/BenLangmead/bowtie.git Repository-Browse: https://github.com/BenLangmead/bowtie View it on GitLab: https://salsa.debian.org/med-team/bowtie/-/commit/344c83aabf06f30804d26ffdb9492fd11756946e -- View it on GitLab: https://salsa.debian.org/med-team/bowtie/-/commit/344c83aabf06f30804d26ffdb9492fd11756946e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bowtie2][master] Update metadata - indent plus ref to guix
Steffen Möller pushed to branch master at Debian Med / bowtie2 Commits: 1dd8cdbe by Steffen Möller at 2021-03-06T22:59:42+00:00 Update metadata - indent plus ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -3,22 +3,24 @@ Bug-Submit: https://github.com/BenLangmead/bowtie2/issues/new Repository: https://github.com/BenLangmead/bowtie.git Repository-Browse: https://github.com/BenLangmead/bowtie2 Reference: - Author: Ben Langmead and Steven L Salzberg - Title: Fast gapped-read alignment with Bowtie 2 - Journal: Nature Methods - Year: 2012 - Volume: 9 - Pages: 357–359 - DOI: 10.1038/nmeth.1923 - PMID: 22388286 - URL: http://www.nature.com/nmeth/journal/v9/n4/abs/nmeth.1923.html - ISSN: 1548-7105 + - Author: Ben Langmead and Steven L Salzberg + Title: Fast gapped-read alignment with Bowtie 2 + Journal: Nature Methods + Year: 2012 + Volume: 9 + Pages: 357–359 + DOI: 10.1038/nmeth.1923 + PMID: 22388286 + URL: http://www.nature.com/nmeth/journal/v9/n4/abs/nmeth.1923.html + ISSN: 1548-7105 Registry: - - Name: SciCrunch -Entry: SCR_005476 - - Name: OMICtools -Entry: OMICS_31633 - - Name: bio.tools -Entry: bowtie2 - - Name: conda:bioconda -Entry: bowtie2 + - Name: SciCrunch + Entry: SCR_005476 + - Name: OMICtools + Entry: OMICS_31633 + - Name: bio.tools + Entry: bowtie2 + - Name: conda:bioconda + Entry: bowtie2 + - Name: guix + Entry: bowtie View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/commit/1dd8cdbe6e754128e3fa95463f2eb7b3923379d8 -- View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/commit/1dd8cdbe6e754128e3fa95463f2eb7b3923379d8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bamtools][master] Update metadata - indent and ref to guix
Steffen Möller pushed to branch master at Debian Med / bamtools Commits: 37913b3e by Steffen Möller at 2021-03-06T22:56:48+00:00 Update metadata - indent and ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,29 +1,31 @@ Bug-Submit: https://github.com/pezmaster31/bamtools/issues/new Reference: -- Author: > + - Author: > Derek W. Barnett and Erik K. Garrison and Aaron R. Quinlan and Michael P. Stromberg and Gabor T. Marth - Title: > + Title: > BamTools: a C++ API and toolkit for analyzing and managing BAM files - Journal: Bioinformatics - Year: 2011 - Volume: 27 - Number: 12 - Pages: 1691-2 - DOI: 10.1093/bioinformatics/btr174 - PMID: 21493652 - URL: http://bioinformatics.oxfordjournals.org/content/27/12/1691 - eprint: > + Journal: Bioinformatics + Year: 2011 + Volume: 27 + Number: 12 + Pages: 1691-2 + DOI: 10.1093/bioinformatics/btr174 + PMID: 21493652 + URL: http://bioinformatics.oxfordjournals.org/content/27/12/1691 + eprint: > http://bioinformatics.oxfordjournals.org/content/27/12/1691.full.pdf+html Registry: -- Name: OMICtools - Entry: OMICS_11315 -- Name: SciCrunch - Entry: SCR_015987 -- Name: bio.tools - Entry: BamTools -- Name: conda:bioconda - Entry: bamtools + - Name: OMICtools + Entry: OMICS_11315 + - Name: SciCrunch + Entry: SCR_015987 + - Name: bio.tools + Entry: BamTools + - Name: conda:bioconda + Entry: bamtools + - Name: guix + Entry: bamtools Repository: https://github.com/pezmaster31/bamtools.git Bug-Database: https://github.com/pezmaster31/bamtools/issues Repository-Browse: https://github.com/pezmaster31/bamtools View it on GitLab: https://salsa.debian.org/med-team/bamtools/-/commit/37913b3e5b1cc8cefd990698632d69f4d7e96fc3 -- View it on GitLab: https://salsa.debian.org/med-team/bamtools/-/commit/37913b3e5b1cc8cefd990698632d69f4d7e96fc3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][master] Update metadata - added ref to guix
Steffen Möller pushed to branch master at Debian Med / rna-star Commits: 87045665 by Steffen Möller at 2021-03-06T19:45:43+00:00 Update metadata - added ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -24,5 +24,7 @@ Registry: Entry: SCR_015899 - Name: conda:bioconda Entry: star + - Name: guix +Entry: star Repository: https://github.com/alexdobin/STAR.git Repository-Browse: https://github.com/alexdobin/STAR View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/87045665719635f17177305b45c653b13d02ea33 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/87045665719635f17177305b45c653b13d02ea33 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/samtools][master] Update metadata - added ref to guix
Steffen Möller pushed to branch master at Debian Med / samtools Commits: a7be9a5e by Steffen Möller at 2021-03-06T19:42:50+00:00 Update metadata - added ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -2,28 +2,30 @@ Bug-Database: https://github.com/samtools/samtools/issues Bug-Submit: https://github.com/samtools/samtools/issues/new Changelog: https://raw.github.com/samtools/samtools/HEAD/NEWS Reference: - author: > + - Author: > Heng Li and Bob Handsaker and Alec Wysoker and Tim Fennell and Jue Ruan and Nils Homer and Gabor Marth and Goncalo Abecasis and Richard Durbin and 1000 Genome Project Data Processing Subgroup - title: The Sequence Alignment/Map (SAM) Format and SAMtools - journal: Bioinformatics - volume: 25 - number: 16 - pages: 2078-2079 - doi: 10.1093/bioinformatics/btp352 - PMID: 19505943 - year: 2009 - URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp352v1 - eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf + Title: The Sequence Alignment/Map (SAM) Format and SAMtools + Journal: Bioinformatics + Volume: 25 + Number: 16 + Pages: 2078-2079 + DOI: 10.1093/bioinformatics/btp352 + PMID: 19505943 + Year: 2009 + URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp352v1 + eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf Repository: https://github.com/samtools/samtools.git Registry: -- Name: bio.tools - Entry: samtools -- Name: SciCrunch - Entry: SCR_002105 -- Name: OMICtools - Entry: OMICS_00090 -- Name: conda:bioconda - Entry: samtools + - Name: bio.tools + Entry: samtools + - Name: SciCrunch + Entry: SCR_002105 + - Name: OMICtools + Entry: OMICS_00090 + - Name: conda:bioconda + Entry: samtools + - Name: guix + Entry: samtools Repository-Browse: https://github.com/samtools/samtools View it on GitLab: https://salsa.debian.org/med-team/samtools/-/commit/a7be9a5e7302b28e70dbe3559ffa2a2a3ea19f86 -- View it on GitLab: https://salsa.debian.org/med-team/samtools/-/commit/a7be9a5e7302b28e70dbe3559ffa2a2a3ea19f86 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sambamba][master] Update metadata - added ref to guix, fixed indent
Steffen Möller pushed to branch master at Debian Med / sambamba Commits: 5b6a9408 by Steffen Möller at 2021-03-06T19:40:15+00:00 Update metadata - added ref to guix, fixed indent - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,27 +1,31 @@ Bug-Database: https://github.com/lomereiter/sambamba/issues Bug-Submit: https://github.com/lomereiter/sambamba/issues/new Reference: - Author: > + - Author: > Artem Tarasov and Albert J. Vilella and Edwin Cuppen and Isaac J. Nijman and Pjotr Prins - Title: 'Sambamba: fast processing of NGS alignment formats' - Journal: Bioinformatics - Year: 2015 - Volume: 31 - Number: 12 - Pages: 2032-2034 - DOI: 10.1093/bioinformatics/btv098 - PMID: 25697820 - URL: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv098 - eprint: https://academic.oup.com/bioinformatics/article-pdf/31/12/2032/568750/btv098.pdf + Title: 'Sambamba: fast processing of NGS alignment formats' + Journal: Bioinformatics + Year: 2015 + Volume: 31 + Number: 12 + Pages: 2032-2034 + DOI: 10.1093/bioinformatics/btv098 + PMID: 25697820 + URL: "https://academic.oup.com/bioinformatics/article-lookup/doi/\ +10.1093/bioinformatics/btv098" + eprint: "https://academic.oup.com/bioinformatics/article-pdf/\ +31/12/2032/568750/btv098.pdf" Registry: -- Name: bio.tools - Entry: Sambamba -- Name: OMICtools - Entry: OMICS_07586 -- Name: SciCrunch - Entry: NA -- Name: conda:bioconda - Entry: sambamba + - Name: bio.tools + Entry: Sambamba + - Name: OMICtools + Entry: OMICS_07586 + - Name: SciCrunch + Entry: NA + - Name: conda:bioconda + Entry: sambamba + - Name: guix + Entry: sambamba Repository: https://github.com/lomereiter/sambamba.git Repository-Browse: https://github.com/lomereiter/sambamba View it on GitLab: https://salsa.debian.org/med-team/sambamba/-/commit/5b6a940810e4a2417367a72476a4725178fcb53e -- View it on GitLab: https://salsa.debian.org/med-team/sambamba/-/commit/5b6a940810e4a2417367a72476a4725178fcb53e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/salmon][master] Update metadata - added ref to guix
Steffen Möller pushed to branch master at Debian Med / salmon Commits: 83ee7dfe by Steffen Möller at 2021-03-06T19:37:46+00:00 Update metadata - added ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -33,3 +33,5 @@ Registry: Entry: NA - Name: conda:bioconda Entry: salmon + - Name: guix + Entry: salmon View it on GitLab: https://salsa.debian.org/med-team/salmon/-/commit/83ee7dfe75e9583d613312739255ba8c2dbccb6d -- View it on GitLab: https://salsa.debian.org/med-team/salmon/-/commit/83ee7dfe75e9583d613312739255ba8c2dbccb6d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sailfish][master] Update metadata - added ref to guix
Steffen Möller pushed to branch master at Debian Med / sailfish Commits: d23e86ad by Steffen Möller at 2021-03-06T19:36:56+00:00 Update metadata - added ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -18,3 +18,5 @@ Registry: Entry: sailfish - Name: SciCrunch Entry: NA + - Name: guix +Entry: sailfish View it on GitLab: https://salsa.debian.org/med-team/sailfish/-/commit/d23e86ade889596763e9c2929f592a846f5c2566 -- View it on GitLab: https://salsa.debian.org/med-team/sailfish/-/commit/d23e86ade889596763e9c2929f592a846f5c2566 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-cutadapt][master] Update metadata - fixing indent
Steffen Möller pushed to branch master at Debian Med / python-cutadapt Commits: 3f7978b4 by Steffen Möller at 2021-03-06T19:34:48+00:00 Update metadata - fixing indent - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,28 +1,28 @@ Reference: -- Author: Marcel Martin - Title: > -Cutadapt removes adapter sequences from high-throughput sequencing -reads - Journal: EMBnet.journal - Year: 2015 - Volume: 17 - Number: 1 - Pages: 10-12 - DOI: 10.14806/ej.17.1.200 - URL: http://journal.embnet.org/index.php/embnetjournal/article/view/200 - eprint: > -http://journal.embnet.org/index.php/embnetjournal/article/view/200/458 + - Author: Marcel Martin + Title: > + Cutadapt removes adapter sequences from high-throughput sequencing + reads + Journal: EMBnet.journal + Year: 2015 + Volume: 17 + Number: 1 + Pages: 10-12 + DOI: 10.14806/ej.17.1.200 + URL: http://journal.embnet.org/index.php/embnetjournal/article/view/200 + eprint: > + http://journal.embnet.org/index.php/embnetjournal/article/view/200/458 Registry: -- Name: OMICtools - Entry: OMICS_01086 -- Name: bio.tools - Entry: cutadapt -- Name: SciCrunch - Entry: SCR_011841 -- Name: conda:bioconda - Entry: cutadapt -- Name: guix - Entry: cutadapt + - Name: OMICtools + Entry: OMICS_01086 + - Name: bio.tools + Entry: cutadapt + - Name: SciCrunch + Entry: SCR_011841 + - Name: conda:bioconda + Entry: cutadapt + - Name: guix + Entry: cutadapt Bug-Database: https://github.com/marcelm/cutadapt/issues Bug-Submit: https://github.com/marcelm/cutadapt/issues/new Repository: https://github.com/marcelm/cutadapt.git View it on GitLab: https://salsa.debian.org/med-team/python-cutadapt/-/commit/3f7978b4e2fb49ce0522af82692a71068635b642 -- View it on GitLab: https://salsa.debian.org/med-team/python-cutadapt/-/commit/3f7978b4e2fb49ce0522af82692a71068635b642 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-cutadapt][master] Update metadata - added to to guix
Steffen Möller pushed to branch master at Debian Med / python-cutadapt Commits: 372b4194 by Steffen Möller at 2021-03-06T19:28:18+00:00 Update metadata - added to to guix Someone has a different opinion on indenting yaml files here. - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -21,6 +21,8 @@ Registry: Entry: SCR_011841 - Name: conda:bioconda Entry: cutadapt +- Name: guix + Entry: cutadapt Bug-Database: https://github.com/marcelm/cutadapt/issues Bug-Submit: https://github.com/marcelm/cutadapt/issues/new Repository: https://github.com/marcelm/cutadapt.git View it on GitLab: https://salsa.debian.org/med-team/python-cutadapt/-/commit/372b419431425266be4cc5a6ac1d2fd309622914 -- View it on GitLab: https://salsa.debian.org/med-team/python-cutadapt/-/commit/372b419431425266be4cc5a6ac1d2fd309622914 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/vcftools][master] Update metadata - added ref to guix
Steffen Möller pushed to branch master at Debian Med / vcftools Commits: 7ba84019 by Steffen Möller at 2021-03-06T19:24:02+00:00 Update metadata - added ref to guix - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -27,5 +27,7 @@ Registry: Entry: vcftools - Name: conda:bioconda Entry: vcftools + - Name: guix +Entry: vcftools Repository: https://github.com/vcftools/vcftools.git Repository-Browse: https://github.com/vcftools/vcftools View it on GitLab: https://salsa.debian.org/med-team/vcftools/-/commit/7ba8401958ff074f3abd0009902950ffba21c587 -- View it on GitLab: https://salsa.debian.org/med-team/vcftools/-/commit/7ba8401958ff074f3abd0009902950ffba21c587 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-bx] Pushed new tag upstream/0.8.9
Steffen Möller pushed new tag upstream/0.8.9 at Debian Med / python-bx -- View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/tree/upstream/0.8.9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-bx] Pushed new tag debian/0.8.9-1
Steffen Möller pushed new tag debian/0.8.9-1 at Debian Med / python-bx -- View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/tree/debian/0.8.9-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-bx][pristine-tar] pristine-tar data for python-bx_0.8.9.orig.tar.gz
Steffen Möller pushed to branch pristine-tar at Debian Med / python-bx Commits: 8df8340e by Steffen Moeller at 2021-02-24T21:45:57+01:00 pristine-tar data for python-bx_0.8.9.orig.tar.gz - - - - - 2 changed files: - + python-bx_0.8.9.orig.tar.gz.delta - + python-bx_0.8.9.orig.tar.gz.id Changes: = python-bx_0.8.9.orig.tar.gz.delta = Binary files /dev/null and b/python-bx_0.8.9.orig.tar.gz.delta differ = python-bx_0.8.9.orig.tar.gz.id = @@ -0,0 +1 @@ +3e18bf54d00d8bea69501f71b49378b8732abda6 View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/commit/8df8340e3731016f97d857823ac14240ab5e8d73 -- View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/commit/8df8340e3731016f97d857823ac14240ab5e8d73 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][pristine-tar] pristine-tar data for rna-star_2.7.8a+dfsg.orig.tar.xz
Steffen Möller pushed to branch pristine-tar at Debian Med / rna-star Commits: ae5b2d4a by Steffen Moeller at 2021-02-23T19:14:42+01:00 pristine-tar data for rna-star_2.7.8a+dfsg.orig.tar.xz - - - - - 2 changed files: - + rna-star_2.7.8a+dfsg.orig.tar.xz.delta - + rna-star_2.7.8a+dfsg.orig.tar.xz.id Changes: = rna-star_2.7.8a+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/rna-star_2.7.8a+dfsg.orig.tar.xz.delta differ = rna-star_2.7.8a+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +f4956ab656bcacf82bc7504fdbcc06a68f56f370 View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/ae5b2d4a2cb4673889bd43c2145623fd76477597 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/ae5b2d4a2cb4673889bd43c2145623fd76477597 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][upstream] New upstream version 2.7.8a+dfsg
Steffen Möller pushed to branch upstream at Debian Med / rna-star Commits: a1fee817 by Steffen Moeller at 2021-02-23T19:14:41+01:00 New upstream version 2.7.8a+dfsg - - - - - 30 changed files: - CHANGES.md - README.md - RELEASEnotes.md - doc/STARmanual.pdf - docs/STARsolo.md - extras/doc-latex/STARmanual.tex - extras/doc-latex/parametersDefault.tex - extras/docker/Dockerfile - extras/scripts/tagXSstrandedData.awk - source/BAMfunctions.cpp - source/BAMfunctions.h - + source/ClipCR4.cpp - + source/ClipCR4.h - + source/ClipMate.h - + source/ClipMate_clip.cpp - + source/ClipMate_clipChunk.cpp - + source/ClipMate_initialize.cpp - source/GTF.cpp - source/Genome_genomeOutLoad.cpp - source/IncludeDefine.h - source/Makefile - source/OutSJ.cpp - source/Parameters.cpp - source/Parameters.h - + source/ParametersClip.h - + source/ParametersClip_initialize.cpp - source/ParametersSolo.cpp - source/ParametersSolo.h - source/Parameters_readFilesInit.cpp - source/Parameters_samAttributes.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/a1fee8172a79c2fbda8a73d03b845576c01acd47 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/a1fee8172a79c2fbda8a73d03b845576c01acd47 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][master] 5 commits: routine-update: New upstream version
Steffen Möller pushed to branch master at Debian Med / rna-star Commits: 327466cd by Steffen Moeller at 2021-02-23T19:14:40+01:00 routine-update: New upstream version - - - - - a1fee817 by Steffen Moeller at 2021-02-23T19:14:41+01:00 New upstream version 2.7.8a+dfsg - - - - - c127290d by Steffen Moeller at 2021-02-23T19:14:42+01:00 Update upstream source from tag upstream/2.7.8a+dfsg Update to upstream version 2.7.8a+dfsg with Debian dir 7c9f7eab593a40f0bacef65041127999353f89ea - - - - - c8d14d37 by Steffen Moeller at 2021-02-23T19:17:59+01:00 routine-update: Ready to upload to unstable - - - - - b81811f3 by Steffen Moeller at 2021-02-23T19:25:03+01:00 New upstream version. - - - - - 30 changed files: - CHANGES.md - README.md - RELEASEnotes.md - debian/changelog - debian/patches/donotuse_own_htslib.patch - debian/patches/mips_shm_noreserve.patch - debian/rules - doc/STARmanual.pdf - docs/STARsolo.md - extras/doc-latex/STARmanual.tex - extras/doc-latex/parametersDefault.tex - extras/docker/Dockerfile - extras/scripts/tagXSstrandedData.awk - source/BAMfunctions.cpp - source/BAMfunctions.h - + source/ClipCR4.cpp - + source/ClipCR4.h - + source/ClipMate.h - + source/ClipMate_clip.cpp - + source/ClipMate_clipChunk.cpp - + source/ClipMate_initialize.cpp - source/GTF.cpp - source/Genome_genomeOutLoad.cpp - source/IncludeDefine.h - source/Makefile - source/OutSJ.cpp - source/Parameters.cpp - source/Parameters.h - + source/ParametersClip.h - + source/ParametersClip_initialize.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/09fbba6ba7a5e9d61673becbc59b8bc1f9282beb...b81811f3ec802e7056a90c0376fcb6c54f12a1d7 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/09fbba6ba7a5e9d61673becbc59b8bc1f9282beb...b81811f3ec802e7056a90c0376fcb6c54f12a1d7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star] Pushed new tag upstream/2.7.8a+dfsg
Steffen Möller pushed new tag upstream/2.7.8a+dfsg at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/upstream/2.7.8a+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star] Pushed new tag debian/2.7.8a+dfsg-1
Steffen Möller pushed new tag debian/2.7.8a+dfsg-1 at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/debian/2.7.8a+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/policy][master] Update policy.rst - gave ref to https://badges.debian.net/
Steffen Möller pushed to branch master at Debian Med / policy Commits: f6351db6 by Steffen Möller at 2021-02-23T17:59:51+00:00 Update policy.rst - gave ref to https://badges.debian.net/ - - - - - 1 changed file: - policy.rst Changes: = policy.rst = @@ -58,7 +58,9 @@ of the original English versions, too. For these, though, you need access to Debian Med's source code repository. Very welcome are tutorials that guide Debian users towards the use of packages to their immediate benefit. You may also consider to write respective articles -for Magazines, be they online or in print. +for Magazines, be they online or in print. Or just help point the developers +of a software to the Debian package and suggest respective link to their +home page, maybe supported by a badge from https://badges.debian.net/. Membership -- View it on GitLab: https://salsa.debian.org/med-team/policy/-/commit/f6351db6964bc9fe56508892b751964b384a9b1c -- View it on GitLab: https://salsa.debian.org/med-team/policy/-/commit/f6351db6964bc9fe56508892b751964b384a9b1c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/minia][master] 2 commits: Wording. Added myself to uploaders.
Steffen Möller pushed to branch master at Debian Med / minia
Commits:
6b22ed14 by Steffen Moeller at 2021-02-16T16:14:36+01:00
Wording. Added myself to uploaders.
- - - - -
e30eaf4e by Steffen Moeller at 2021-02-16T19:33:20+01:00
Adjust dep to patched version of gatb
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/rules
- debian/watch
Changes:
=
debian/changelog
=
@@ -3,14 +3,10 @@ minia (3.2.4-1) UNRELEASED; urgency=medium
* Team upload.
* New upstream version
* debhelper-compat 13 (routine-update)
+ * Adjusted build dependencies to patched version of gatb 1.4.2
+ * d/rules - improved clean
* d/watch - using regular releases again (up from 3.2.1 to 3.2.4)
-BLOCKER: FTBFS needs new gatb version
- /usr/include/gatb/tools/math/Integer.hpp:84:71: required from ‘static
void gatb::core::tools::math::IntegerTemplate::apply(size_t,
Parameter) [with Functor = MiniaFunctor; Parameter = Parameter; IntegerList =
boost::mpl::vector4, mpl_::int_<64>, mpl_::int_<96>,
mpl_::int_<128> >; size_t = long unsigned int]’
- /med-team/minia/src/Minia.cpp:170:65: required from here
- /med-team/minia/src/Minia.cpp:312:62: error: ‘class
gatb::core::debruijn::impl::GraphUnitigsTemplate<128>’ has no member named
‘_nbSolidKmers’
-
-
-- Steffen Moeller Mon, 10 Aug 2020 19:16:26 +0200
minia (3.2.1+git20200522.4960a99-1) unstable; urgency=medium
=
debian/control
=
@@ -1,7 +1,8 @@
Source: minia
Maintainer: Debian Med Packaging Team
Uploaders: Olivier Sallou ,
- Andreas Tille
+ Andreas Tille ,
+ Steffen Moeller
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -9,9 +10,9 @@ Build-Depends: debhelper-compat (= 13),
bc,
zlib1g-dev,
libboost-dev,
- libgatbcore-dev (>= 1.4.1+git20191130.664696c),
+ libgatbcore-dev (>= 1.4.2-7),
libhdf5-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/minia
Vcs-Git: https://salsa.debian.org/med-team/minia.git
Homepage: http://minia.genouest.org/
@@ -26,9 +27,21 @@ Depends: ${misc:Depends},
Recommends: samtools
Suggests: bandage
Description: short-read biological sequence assembler
- Short-read DNA sequence assembler based on a de Bruijn graph,
- capable of assembling a human genome on a desktop computer in a day.
+ What was referred to as "next-generation" DNA sequencing up to
+ the year 2020 delivered only "short" reads up to ~600 base pairs
+ in length that would then have to be puzzled by random overlaps
+ in their sequence towards a complete genome. This is the genome
+ assembly. And there are many biological pitfalls on long stretches
+ of low complexity regions and copy number variations and other
+ sorts of redundancies that render this difficult.
+ .
+ This package provides a short-read DNA sequence assembler based on a
+ de Bruijn graph, capable of assembling a human genome on a desktop
+ computer in a day.
+ .
+ The output of Minia is a set of contigs, i.e. stretches of gap-free
+ linear overlaps of short reads. In the best possible case this is
+ a whole chromosome.
.
- The output of Minia is a set of contigs.
Minia produces results of similar contiguity and accuracy to other
de Bruijn assemblers (e.g. Velvet).
=
debian/rules
=
@@ -11,3 +11,4 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
override_dh_clean:
dh_clean
rm -f minia src/build_info.hpp
+ rm -rf obj-x86_64-linux-gnu src/build_info.hpp
=
debian/watch
=
@@ -3,6 +3,6 @@ version=4
https://github.com/GATB/minia/releases
.*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
# Once upon a time, the released version was not compatible with gatb-core
1.4.1+git20191130.664696c+dfsg
-# That is we sticked to latest Git commit back then.
+# That is why we sticked to latest Git commit back then.
#opts="mode=git,pretty=3.2.1+git%cd.%h" \
#https://github.com/GATB/minia.git HEAD
View it on GitLab:
https://salsa.debian.org/med-team/minia/-/compare/0eaa42246bcb41e6d6f7e13e8e08e1f8f3dcb0ee...e30eaf4e8d414d7080712ce424c266f8ece3bdfd
--
View it on GitLab:
https://salsa.debian.org/med-team/minia/-/compare/0eaa42246bcb41e6d6f7e13e8e08e1f8f3dcb0ee...e30eaf4e8d414d7080712ce424c266f8ece3bdfd
You're receiving this email because of your account on salsa.debian.org.
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[med-svn] [Git][med-team/bioawk] Pushed new tag debian/1.0-1
Steffen Möller pushed new tag debian/1.0-1 at Debian Med / bioawk -- View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/tree/debian/1.0-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bioawk] Pushed new tag upstream/1.0
Steffen Möller pushed new tag upstream/1.0 at Debian Med / bioawk -- View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/tree/upstream/1.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bioawk] Deleted tag upstream/1.0
Steffen Möller deleted tag upstream/1.0 at Debian Med / bioawk -- You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bioawk] Pushed new branch pristine-tar
Steffen Möller pushed new branch pristine-tar at Debian Med / bioawk -- View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/tree/pristine-tar You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bioawk][upstream] New upstream version 1.0
Steffen Möller pushed to branch upstream at Debian Med / bioawk Commits: ab0ab07f by Steffen Möller at 2021-02-12T02:46:31+01:00 New upstream version 1.0 - - - - - 0 changed files: Changes: View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/commit/ab0ab07f83bbece56fafb30bdcc04fde2c89b51a -- View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/commit/ab0ab07f83bbece56fafb30bdcc04fde2c89b51a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bioawk][master] 3 commits: Optics - thanks Juhani
Steffen Möller pushed to branch master at Debian Med / bioawk
Commits:
58f9225a by Steffen Möller at 2021-02-12T02:45:25+01:00
Optics - thanks Juhani
- - - - -
ab0ab07f by Steffen Möller at 2021-02-12T02:46:31+01:00
New upstream version 1.0
- - - - -
f8088b37 by Steffen Möller at 2021-02-12T02:46:31+01:00
Update upstream source from tag upstream/1.0
Update to upstream version 1.0
with Debian dir ff461e435cde85e6997d8ae1388d4fba0e5c48f5
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -1,4 +1,4 @@
-bioawk (1.0-1) UNRELEASED; urgency=medium
+bioawk (1.0-1) unstable; urgency=medium
* Initial release (Closes: #982544)
=
debian/control
=
@@ -2,7 +2,8 @@ Source: bioawk
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team
-Uploaders: Steffen Moeller , Nilesh Patra
+Uploaders: Steffen Moeller ,
+ Nilesh Patra
Build-Depends: debhelper-compat (= 13),
bison,
libz-dev
@@ -16,7 +17,7 @@ Package: bioawk
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: extension of awk for biological sequence analysis
- Bioawk is an extension to [Brian Kernighan's awk], adding the support of
+ Bioawk is an extension to Brian Kernighan's awk, adding the support of
several common biological data formats, including optionally gzip'ed BED, GFF,
SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a
few built-in functions and an command line option to use TAB as the
View it on GitLab:
https://salsa.debian.org/med-team/bioawk/-/compare/2e7f94245e48ec22c99bd7e256dc9428ea0b341c...f8088b371c4b2bc9fd0123d11f80b35c64b73a7f
--
View it on GitLab:
https://salsa.debian.org/med-team/bioawk/-/compare/2e7f94245e48ec22c99bd7e256dc9428ea0b341c...f8088b371c4b2bc9fd0123d11f80b35c64b73a7f
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[med-svn] [Git][med-team/conda] Pushed new tag upstream/4.9.2+dfsg
Steffen Möller pushed new tag upstream/4.9.2+dfsg at Debian Med / conda -- View it on GitLab: https://salsa.debian.org/med-team/conda/-/tree/upstream/4.9.2+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/conda][pristine-tar] pristine-tar data for conda_4.9.2+dfsg.orig.tar.xz
Steffen Möller pushed to branch pristine-tar at Debian Med / conda Commits: 0b91488c by Steffen Moeller at 2021-02-11T11:04:26+01:00 pristine-tar data for conda_4.9.2+dfsg.orig.tar.xz - - - - - 2 changed files: - + conda_4.9.2+dfsg.orig.tar.xz.delta - + conda_4.9.2+dfsg.orig.tar.xz.id Changes: = conda_4.9.2+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/conda_4.9.2+dfsg.orig.tar.xz.delta differ = conda_4.9.2+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +3bdab3b33de5950319d59c0bfef97223b21315ed View it on GitLab: https://salsa.debian.org/med-team/conda/-/commit/0b91488c0e8e11c84ccd3450cabdb5147461b4bd -- View it on GitLab: https://salsa.debian.org/med-team/conda/-/commit/0b91488c0e8e11c84ccd3450cabdb5147461b4bd You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/conda][master] 3 commits: New upstream version 4.9.2+dfsg
Steffen Möller pushed to branch master at Debian Med / conda Commits: b5385062 by Steffen Moeller at 2021-02-11T11:03:38+01:00 New upstream version 4.9.2+dfsg - - - - - bf91e4d6 by Steffen Moeller at 2021-02-11T11:04:27+01:00 Update upstream source from tag upstream/4.9.2+dfsg Update to upstream version 4.9.2+dfsg with Debian dir 33c9f304e945099b58cdd9c2d52edde81f68cfe3 - - - - - 27d4e538 by Steffen Moeller at 2021-02-11T11:17:16+01:00 Adjusting patches, a bit of clean-up - - - - - 29 changed files: - .cla-signers - .gitattributes - + .github/workflows/ci.yml - CHANGELOG.md - README.rst - − appveyor.yml - + ci/build_docs.sh - + ci/integration_tests.sh - + ci/unit_test.sh - − circle.yml - conda.recipe/meta.yaml - conda/_vendor/auxlib/compat.py - conda/_vendor/auxlib/configuration.py - conda/_vendor/auxlib/logz.py - conda/_vendor/cpuinfo.py - conda/_vendor/tqdm/LICENSE - conda/_vendor/tqdm/__init__.py - conda/_vendor/tqdm/__main__.py - conda/_vendor/tqdm/_main.py - conda/_vendor/tqdm/_monitor.py - conda/_vendor/tqdm/_tqdm.py - conda/_vendor/tqdm/_utils.py - conda/_vendor/tqdm/_version.py - + conda/_vendor/tqdm/asyncio.py - + conda/_vendor/tqdm/auto.py - + conda/_vendor/tqdm/cli.py - + conda/_vendor/tqdm/contrib/__init__.py - + conda/_vendor/tqdm/contrib/concurrent.py - + conda/_vendor/tqdm/contrib/itertools.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/conda/-/compare/6348f41fbdcf7db1d9564475e0750fb04532d726...27d4e5380513588023678412a3819c11696c2d4b -- View it on GitLab: https://salsa.debian.org/med-team/conda/-/compare/6348f41fbdcf7db1d9564475e0750fb04532d726...27d4e5380513588023678412a3819c11696c2d4b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/conda][upstream] New upstream version 4.9.2+dfsg
Steffen Möller pushed to branch upstream at Debian Med / conda Commits: b5385062 by Steffen Moeller at 2021-02-11T11:03:38+01:00 New upstream version 4.9.2+dfsg - - - - - 29 changed files: - .cla-signers - .gitattributes - + .github/workflows/ci.yml - CHANGELOG.md - README.rst - − appveyor.yml - + ci/build_docs.sh - + ci/integration_tests.sh - + ci/unit_test.sh - − circle.yml - conda.recipe/meta.yaml - conda/_vendor/auxlib/compat.py - conda/_vendor/auxlib/configuration.py - conda/_vendor/auxlib/logz.py - conda/_vendor/cpuinfo.py - conda/_vendor/tqdm/LICENSE - conda/_vendor/tqdm/__init__.py - conda/_vendor/tqdm/__main__.py - conda/_vendor/tqdm/_main.py - conda/_vendor/tqdm/_monitor.py - conda/_vendor/tqdm/_tqdm.py - conda/_vendor/tqdm/_utils.py - conda/_vendor/tqdm/_version.py - + conda/_vendor/tqdm/asyncio.py - + conda/_vendor/tqdm/auto.py - + conda/_vendor/tqdm/cli.py - + conda/_vendor/tqdm/contrib/__init__.py - + conda/_vendor/tqdm/contrib/concurrent.py - + conda/_vendor/tqdm/contrib/itertools.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/conda/-/commit/b5385062a3f5368f9c38cb8cb7363c0365455989 -- View it on GitLab: https://salsa.debian.org/med-team/conda/-/commit/b5385062a3f5368f9c38cb8cb7363c0365455989 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/conda][master] New upstream version.
Steffen Möller pushed to branch master at Debian Med / conda Commits: 6348f41f by Steffen Moeller at 2021-02-11T11:01:12+01:00 New upstream version. - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = @@ -1,3 +1,9 @@ +conda (4.9.2+dfsg-1~rc0) UNRELEASED; urgency=medium + + * New upstream release. + + -- Steffen Moeller Wed, 10 Feb 2021 20:31:05 +0100 + conda (4.8.2+dfsg-1~rc0) experimental; urgency=medium * Initial release (Closes: #926416) = debian/control = @@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 12), python3-mock , xonsh, conda-package-handling , -Standards-Version: 4.4.1 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/conda Vcs-Git: https://salsa.debian.org/med-team/conda.git Homepage: https://conda.io/ @@ -38,3 +38,10 @@ Description: OS-agnostic, system-level binary package manager and ecosystem used for other systems as well. Conda makes environments first-class citizens, making it easy to create independent environments even for C libraries. + . + This package needs a bit of extra love to smoothen its applicability in + a pure Debian environment, but all the functionality of the conda software + infrastructure is available - except for the typical miniconda seed. + This should not be required since Debian offers everything already, but + it is yet a bit edgy as in files expected below /usr that are not + existing - and should not be expected at that location in the first place. View it on GitLab: https://salsa.debian.org/med-team/conda/-/commit/6348f41fbdcf7db1d9564475e0750fb04532d726 -- View it on GitLab: https://salsa.debian.org/med-team/conda/-/commit/6348f41fbdcf7db1d9564475e0750fb04532d726 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][pristine-tar] pristine-tar data for bcbio_1.2.6.orig.tar.gz
Steffen Möller pushed to branch pristine-tar at Debian Med / bcbio Commits: 30dab8f6 by Steffen Moeller at 2021-02-10T16:25:03+01:00 pristine-tar data for bcbio_1.2.6.orig.tar.gz - - - - - 2 changed files: - + bcbio_1.2.6.orig.tar.gz.delta - + bcbio_1.2.6.orig.tar.gz.id Changes: = bcbio_1.2.6.orig.tar.gz.delta = Binary files /dev/null and b/bcbio_1.2.6.orig.tar.gz.delta differ = bcbio_1.2.6.orig.tar.gz.id = @@ -0,0 +1 @@ +303c55cd881dea2d942a1cce94cd8b1f273f5212 View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/30dab8f685fff80b5425231b9517b52ec8ea920f -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/30dab8f685fff80b5425231b9517b52ec8ea920f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][master] 3 commits: New upstream version 1.2.6
Steffen Möller pushed to branch master at Debian Med / bcbio Commits: 5c8848ab by Steffen Moeller at 2021-02-10T16:24:07+01:00 New upstream version 1.2.6 - - - - - a4e8977a by Steffen Moeller at 2021-02-10T16:25:03+01:00 Update upstream source from tag upstream/1.2.6 Update to upstream version 1.2.6 with Debian dir 302e32dd03f2c29d4ea15076af5ae9170dc10e54 - - - - - 68261fcd by Steffen Moeller at 2021-02-10T18:29:23+01:00 Upstream accepted patch, added dep on libhts-dev The .so is attempted to be loaded. - - - - - 30 changed files: - HISTORY.md - MANIFEST.in - README.md - bcbio/dragen/dragen.py - bcbio/pipeline/main.py - bcbio/pipeline/rnaseq.py - bcbio/pipeline/run_info.py - bcbio/provenance/programs.py - bcbio/variation/annotation.py - bcbio/variation/vardict.py - config/examples/rnaseq-seqc-getdata.sh - config/examples/rnaseq-seqc.yaml - config/examples/seqc.csv - config/genomes/GRCh37-resources.yaml - config/genomes/hg19-resources.yaml - config/genomes/hg38-resources.yaml - + config/templates/purecn_ton.yaml - config/vcfanno/GRCh37-gemini.conf - config/vcfanno/hg38-gemini.conf - config/vcfanno/somatic.conf - debian/changelog - debian/control - − debian/patches/include_tests - debian/patches/series - docs/contents/bulk_rnaseq.md - docs/contents/configuration.md - docs/contents/installation.md - docs/contents/purecn.md - requirements-conda.txt - requirements.txt The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/bbe5fb17531f381785724476861b81cf9d2eba99...68261fcdb35b8f5d078023944114bc5b465cb884 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/bbe5fb17531f381785724476861b81cf9d2eba99...68261fcdb35b8f5d078023944114bc5b465cb884 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][upstream] New upstream version 1.2.5
Steffen Möller pushed to branch upstream at Debian Med / bcbio Commits: 1c20dafa by Steffen Moeller at 2021-01-26T13:53:56+01:00 New upstream version 1.2.5 - - - - - 30 changed files: - HISTORY.md - MANIFEST.in - README.md - bcbio/bam/__init__.py - bcbio/bam/cram.py - bcbio/chipseq/antibodies.py - bcbio/chipseq/atac.py - bcbio/chipseq/macs2.py - bcbio/chipseq/peaks.py - + bcbio/dragen/__init__.py - + bcbio/dragen/dragen.py - bcbio/heterogeneity/loh.py - bcbio/install.py - bcbio/ngsalign/alignprep.py - bcbio/ngsalign/postalign.py - bcbio/pipeline/datadict.py - bcbio/pipeline/genome.py - bcbio/pipeline/main.py - bcbio/pipeline/rnaseq.py - bcbio/pipeline/run_info.py - bcbio/pipeline/sample.py - bcbio/rnaseq/count.py - bcbio/rnaseq/featureCounts.py - bcbio/rnaseq/salmon.py - + bcbio/scripts/R/bcbio2se.R - + bcbio/scripts/R/se2qc.Rmd - bcbio/structural/__init__.py - bcbio/structural/delly.py - bcbio/structural/lumpy.py - bcbio/structural/purecn.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/1c20dafa2114b4a1649475df5bbb3bd24a22a18c -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/1c20dafa2114b4a1649475df5bbb3bd24a22a18c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][master] 3 commits: New upstream version 1.2.5
Steffen Möller pushed to branch master at Debian Med / bcbio Commits: 1c20dafa by Steffen Moeller at 2021-01-26T13:53:56+01:00 New upstream version 1.2.5 - - - - - 17c33c5a by Steffen Moeller at 2021-01-26T13:54:36+01:00 Update upstream source from tag upstream/1.2.5 Update to upstream version 1.2.5 with Debian dir 170647d8542f5cc09d1688feb0947f06d4cb0f01 - - - - - bbe5fb17 by Steffen Moeller at 2021-01-26T14:22:57+01:00 New upstream version. - - - - - 30 changed files: - HISTORY.md - MANIFEST.in - README.md - bcbio/bam/__init__.py - bcbio/bam/cram.py - bcbio/chipseq/antibodies.py - bcbio/chipseq/atac.py - bcbio/chipseq/macs2.py - bcbio/chipseq/peaks.py - + bcbio/dragen/__init__.py - + bcbio/dragen/dragen.py - bcbio/heterogeneity/loh.py - bcbio/install.py - bcbio/ngsalign/alignprep.py - bcbio/ngsalign/postalign.py - bcbio/pipeline/datadict.py - bcbio/pipeline/genome.py - bcbio/pipeline/main.py - bcbio/pipeline/rnaseq.py - bcbio/pipeline/run_info.py - bcbio/pipeline/sample.py - bcbio/rnaseq/count.py - bcbio/rnaseq/featureCounts.py - bcbio/rnaseq/salmon.py - + bcbio/scripts/R/bcbio2se.R - + bcbio/scripts/R/se2qc.Rmd - bcbio/structural/__init__.py - bcbio/structural/delly.py - bcbio/structural/lumpy.py - bcbio/structural/purecn.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/a48982aa7bca71129decc931487c09ef30496119...bbe5fb17531f381785724476861b81cf9d2eba99 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/a48982aa7bca71129decc931487c09ef30496119...bbe5fb17531f381785724476861b81cf9d2eba99 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][pristine-tar] pristine-tar data for bcbio_1.2.5.orig.tar.gz
Steffen Möller pushed to branch pristine-tar at Debian Med / bcbio Commits: 163bda1e by Steffen Moeller at 2021-01-26T13:54:36+01:00 pristine-tar data for bcbio_1.2.5.orig.tar.gz - - - - - 2 changed files: - + bcbio_1.2.5.orig.tar.gz.delta - + bcbio_1.2.5.orig.tar.gz.id Changes: = bcbio_1.2.5.orig.tar.gz.delta = Binary files /dev/null and b/bcbio_1.2.5.orig.tar.gz.delta differ = bcbio_1.2.5.orig.tar.gz.id = @@ -0,0 +1 @@ +b2089e325c576b69ea1713add4cd192369c372e4 View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/163bda1e66f237eff4f8c967828546d3556f3fd6 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/163bda1e66f237eff4f8c967828546d3556f3fd6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/xxsds-dynamic][master] 2 commits: Fix for resubmission
Steffen Möller pushed to branch master at Debian Med / xxsds-dynamic Commits: dd142aa9 by Steffen Möller at 2020-09-13T19:48:03+02:00 Fix for resubmission - - - - - 79ff5f4c by Steffen Möller at 2021-01-26T12:34:25+01:00 Fixing #980972 on missing changelog trailer - - - - - 2 changed files: - debian/changelog - debian/copyright Changes: = debian/changelog = @@ -1,5 +1,22 @@ -xxsds-dynamic (1.0~alpha.1+2020072524git5390b6c-1) unstable; urgency=medium +xxsds-dynamic (1.0~alpha.1+2020072524git5390b6c-3) unstable; urgency=medium + + * Fixed omitted trailer in d/changelog + +Many thanks go to Logan Rosen for spotting that (Closes: #980972). + + -- Steffen Moeller Tue, 26 Jan 2021 12:31:31 +0100 + +xxsds-dynamic (1.0~alpha.1+2020072524git5390b6c-2) unstable; urgency=medium * Initial release (Closes: #965272) +d/copyright now references the contributions by Erik Garrison +(thanks go to FTPmaster Thorsten for spotting that omission). + + -- Steffen Moeller Sun, 13 Sep 2020 19:48:50 +0200 + +xxsds-dynamic (1.0~alpha.1+2020072524git5390b6c-1) UNRELEASED; urgency=medium + + * Initial submission to main. + -- Steffen Moeller Sat, 18 Jul 2020 16:40:45 +0200 = debian/copyright = @@ -7,6 +7,15 @@ Copyright: 2020 Alan Kuhnle 2017 Nicola Prezza License: MIT +Files: include/dynamic/internal/wm_string.hpp +Copyright: 2019-2020 Erik Garrison +License: MIT + +Files: include/dynamic/internal/hacked_vector.hpp +Copyright: 2019 Nicola Prezza +Erik Garrison +License: MIT + Files: debian/* Copyright: 2020 Steffen Moeller License: MIT View it on GitLab: https://salsa.debian.org/med-team/xxsds-dynamic/-/compare/65b33b0b46d91b92ba43287e8e3701b4d3c6c541...79ff5f4c3b95d8f14e9200f6588620206d98b292 -- View it on GitLab: https://salsa.debian.org/med-team/xxsds-dynamic/-/compare/65b33b0b46d91b92ba43287e8e3701b4d3c6c541...79ff5f4c3b95d8f14e9200f6588620206d98b292 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][upstream] New upstream version 3.4.0+dfsg
Steffen Möller pushed to branch upstream at Debian Med / augustus Commits: d6d05ec1 by Steffen Moeller at 2020-12-22T17:56:24+01:00 New upstream version 3.4.0+dfsg - - - - - 30 changed files: - + .dockerignore - + .github/workflows/examples_test.yml - + .github/workflows/execute_nightly_tests.yml - .gitignore - .travis.yml - Dockerfile - − Dockerfile-cgp-file - − Dockerfile-cgp-mysql - − Dockerfile-cgp-sqlite - Makefile - README.md - auxprogs/Makefile - auxprogs/aln2wig/Makefile - auxprogs/bam2hints/Makefile - auxprogs/bam2wig/Makefile - + auxprogs/bam2wig/README.md - − auxprogs/bam2wig/README.txt - auxprogs/bam2wig/bam2wig.c - − auxprogs/checkTargetSortedness/Makefile - − auxprogs/checkTargetSortedness/checkTargetSortedness.c - auxprogs/compileSpliceCands/Makefile - auxprogs/compileSpliceCands/compileSpliceCands.c - auxprogs/filterBam/src/Makefile - + auxprogs/homGeneMapping/Dockerfile - auxprogs/homGeneMapping/Makefile - auxprogs/homGeneMapping/README.TXT - − auxprogs/homGeneMapping/examples/make.doc - auxprogs/homGeneMapping/include/genome.hh - auxprogs/homGeneMapping/src/Makefile - auxprogs/homGeneMapping/src/genome.cc The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/d6d05ec174bf50c7b86b21b346f7180a5be31e28 -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/d6d05ec174bf50c7b86b21b346f7180a5be31e28 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][master] 8 commits: routine-update: New upstream version
Steffen Möller pushed to branch master at Debian Med / augustus Commits: 76f4e72d by Steffen Moeller at 2020-12-22T17:56:13+01:00 routine-update: New upstream version - - - - - d6d05ec1 by Steffen Moeller at 2020-12-22T17:56:24+01:00 New upstream version 3.4.0+dfsg - - - - - 95fbccb4 by Steffen Moeller at 2020-12-22T18:02:17+01:00 Update upstream source from tag upstream/3.4.0+dfsg Update to upstream version 3.4.0+dfsg with Debian dir 8cb34729c78c01a752d94b4a17208a9970eb6c69 - - - - - dfd3b1f0 by Steffen Moeller at 2020-12-22T18:02:18+01:00 routine-update: Standards-Version: 4.5.1 - - - - - 5acca058 by Steffen Moeller at 2020-12-22T18:02:21+01:00 routine-update: Add salsa-ci file - - - - - f842a4b0 by Steffen Moeller at 2020-12-22T18:02:31+01:00 Use secure URI in Homepage field. Changes-By: lintian-brush Fixes: lintian: homepage-field-uses-insecure-uri See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html - - - - - c8774226 by Steffen Moeller at 2020-12-22T18:02:37+01:00 Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-bug-tracking See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html Fixes: lintian: upstream-metadata-missing-repository See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html - - - - - f6b3fb3b by Steffen Moeller at 2020-12-23T22:24:24+01:00 Upstream adopted quite a bit. - - - - - 30 changed files: - + .dockerignore - + .github/workflows/examples_test.yml - + .github/workflows/execute_nightly_tests.yml - .gitignore - .travis.yml - Dockerfile - − Dockerfile-cgp-file - − Dockerfile-cgp-mysql - − Dockerfile-cgp-sqlite - Makefile - README.md - auxprogs/Makefile - auxprogs/aln2wig/Makefile - auxprogs/bam2hints/Makefile - auxprogs/bam2wig/Makefile - + auxprogs/bam2wig/README.md - − auxprogs/bam2wig/README.txt - auxprogs/bam2wig/bam2wig.c - − auxprogs/checkTargetSortedness/Makefile - − auxprogs/checkTargetSortedness/checkTargetSortedness.c - auxprogs/compileSpliceCands/Makefile - auxprogs/compileSpliceCands/compileSpliceCands.c - auxprogs/filterBam/src/Makefile - + auxprogs/homGeneMapping/Dockerfile - auxprogs/homGeneMapping/Makefile - auxprogs/homGeneMapping/README.TXT - − auxprogs/homGeneMapping/examples/make.doc - auxprogs/homGeneMapping/include/genome.hh - auxprogs/homGeneMapping/src/Makefile - auxprogs/homGeneMapping/src/genome.cc The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/augustus/-/compare/872bc0cde337d6114f0c8ad2d9df227a6a7ae549...f6b3fb3b199d4dd23b41246b6b5b62ff739d9acd -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/compare/872bc0cde337d6114f0c8ad2d9df227a6a7ae549...f6b3fb3b199d4dd23b41246b6b5b62ff739d9acd You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][pristine-tar] pristine-tar data for augustus_3.4.0+dfsg.orig.tar.xz
Steffen Möller pushed to branch pristine-tar at Debian Med / augustus Commits: 5834e945 by Steffen Moeller at 2020-12-22T18:02:17+01:00 pristine-tar data for augustus_3.4.0+dfsg.orig.tar.xz - - - - - 2 changed files: - + augustus_3.4.0+dfsg.orig.tar.xz.delta - + augustus_3.4.0+dfsg.orig.tar.xz.id Changes: = augustus_3.4.0+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/augustus_3.4.0+dfsg.orig.tar.xz.delta differ = augustus_3.4.0+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +49e78c15cd0b2e02d90dc383aab267691bba0683 View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/5834e94573181eddeab876317a360ae3760c79a9 -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/5834e94573181eddeab876317a360ae3760c79a9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-feature-table] Pushed new tag upstream/2020.11.1+dfsg
Steffen Möller pushed new tag upstream/2020.11.1+dfsg at Debian Med / q2-feature-table -- View it on GitLab: https://salsa.debian.org/med-team/q2-feature-table/-/tree/upstream/2020.11.1+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-feature-table] Pushed new tag debian/2020.11.1+dfsg-1
Steffen Möller pushed new tag debian/2020.11.1+dfsg-1 at Debian Med / q2-feature-table -- View it on GitLab: https://salsa.debian.org/med-team/q2-feature-table/-/tree/debian/2020.11.1+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-feature-table][upstream] New upstream version 2020.11.1+dfsg
Steffen Möller pushed to branch upstream at Debian Med / q2-feature-table
Commits:
cc3249d9 by Steffen Moeller at 2020-12-19T20:56:40+01:00
New upstream version 2020.11.1+dfsg
- - - - -
1 changed file:
- q2_feature_table/_version.py
Changes:
=
q2_feature_table/_version.py
=
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
-git_refnames = " (HEAD -> master, tag: 2020.11.0)"
-git_full = "a118c101633ee809fb87fb3d9ce8336dad9df82a"
-git_date = "2020-11-25 17:13:07 +"
+git_refnames = " (tag: 2020.11.1)"
+git_full = "58e0fac843eee4edb39a533dbe4ef534a87a7c0e"
+git_date = "2020-12-05 20:44:52 +"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab:
https://salsa.debian.org/med-team/q2-feature-table/-/commit/cc3249d9d3d14560da45f34eee105e089a05ef35
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-feature-table/-/commit/cc3249d9d3d14560da45f34eee105e089a05ef35
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[med-svn] [Git][med-team/q2-feature-table][pristine-tar] pristine-tar data for q2-feature-table_2020.11.1+dfsg.orig.tar.xz
Steffen Möller pushed to branch pristine-tar at Debian Med / q2-feature-table Commits: 0d22ad6d by Steffen Moeller at 2020-12-19T20:56:40+01:00 pristine-tar data for q2-feature-table_2020.11.1+dfsg.orig.tar.xz - - - - - 2 changed files: - + q2-feature-table_2020.11.1+dfsg.orig.tar.xz.delta - + q2-feature-table_2020.11.1+dfsg.orig.tar.xz.id Changes: = q2-feature-table_2020.11.1+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/q2-feature-table_2020.11.1+dfsg.orig.tar.xz.delta differ = q2-feature-table_2020.11.1+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +7a3a2b8d761935df3bf432e79a1a3f8932285971 View it on GitLab: https://salsa.debian.org/med-team/q2-feature-table/-/commit/0d22ad6d383e71836a6562e0dec69f55d768bc09 -- View it on GitLab: https://salsa.debian.org/med-team/q2-feature-table/-/commit/0d22ad6d383e71836a6562e0dec69f55d768bc09 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-feature-table][master] 5 commits: routine-update: New upstream version
Steffen Möller pushed to branch master at Debian Med / q2-feature-table
Commits:
193e3948 by Steffen Moeller at 2020-12-19T20:56:39+01:00
routine-update: New upstream version
- - - - -
cc3249d9 by Steffen Moeller at 2020-12-19T20:56:40+01:00
New upstream version 2020.11.1+dfsg
- - - - -
b34acca1 by Steffen Moeller at 2020-12-19T20:56:40+01:00
Update upstream source from tag upstream/2020.11.1+dfsg
Update to upstream version 2020.11.1+dfsg
with Debian dir fe8bf83f568d982fbc344419f172c37ec14f1e8d
- - - - -
a25cc300 by Steffen Moeller at 2020-12-19T20:56:46+01:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
e1b25292 by Steffen Moeller at 2020-12-19T20:57:29+01:00
routine-update: Ready to upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/rules
- q2_feature_table/_version.py
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+q2-feature-table (2020.11.1+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Trim trailing whitespace.
+
+ -- Steffen Moeller Sat, 19 Dec 2020 20:56:47 +0100
+
q2-feature-table (2020.11.0+dfsg-1) unstable; urgency=medium
* Team upload.
=
debian/rules
=
@@ -31,4 +31,3 @@ endif
override_dh_auto_clean:
dh_auto_clean
rm -f q2_feature_table.egg-info/PKG-INFO
q2_feature_table.egg-info/SOURCES.txt
q2_feature_table.egg-info/dependency_links.txt
q2_feature_table.egg-info/entry_points.txt
q2_feature_table.egg-info/not-zip-safe q2_feature_table.egg-info/top_level.txt
-
=
q2_feature_table/_version.py
=
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
-git_refnames = " (HEAD -> master, tag: 2020.11.0)"
-git_full = "a118c101633ee809fb87fb3d9ce8336dad9df82a"
-git_date = "2020-11-25 17:13:07 +"
+git_refnames = " (tag: 2020.11.1)"
+git_full = "58e0fac843eee4edb39a533dbe4ef534a87a7c0e"
+git_date = "2020-12-05 20:44:52 +"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab:
https://salsa.debian.org/med-team/q2-feature-table/-/compare/caafe9254c94858bb9fd231aa624d00765d02fcd...e1b25292afcbaa3b484128c2870a5e278eadcf5b
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-feature-table/-/compare/caafe9254c94858bb9fd231aa624d00765d02fcd...e1b25292afcbaa3b484128c2870a5e278eadcf5b
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[med-svn] [Git][med-team/pigx-scrnaseq][pristine-tar] pristine-tar data for pigx-scrnaseq_1.1.7+ds.orig.tar.xz
Steffen Möller pushed to branch pristine-tar at Debian Med / pigx-scrnaseq Commits: e07cb06c by Steffen Moeller at 2020-12-14T00:08:11+01:00 pristine-tar data for pigx-scrnaseq_1.1.7+ds.orig.tar.xz - - - - - 2 changed files: - + pigx-scrnaseq_1.1.7+ds.orig.tar.xz.delta - + pigx-scrnaseq_1.1.7+ds.orig.tar.xz.id Changes: = pigx-scrnaseq_1.1.7+ds.orig.tar.xz.delta = Binary files /dev/null and b/pigx-scrnaseq_1.1.7+ds.orig.tar.xz.delta differ = pigx-scrnaseq_1.1.7+ds.orig.tar.xz.id = @@ -0,0 +1 @@ +bd1d2b77fbc1eef5d13b8579e5f7c4063af7c6a6 View it on GitLab: https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/e07cb06c5f42db4b52c6faa9ea3ee50570e190b3 -- View it on GitLab: https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/e07cb06c5f42db4b52c6faa9ea3ee50570e190b3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/pigx-scrnaseq][master] routine-update: New upstream version
Steffen Möller pushed to branch master at Debian Med / pigx-scrnaseq Commits: 362f4910 by Steffen Moeller at 2020-12-14T00:04:25+01:00 routine-update: New upstream version - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,13 +1,13 @@ -pigx-scrnaseq (1.1.6+ds-1) UNRELEASED; urgency=medium +pigx-scrnaseq (1.1.7+ds-1) UNRELEASED; urgency=medium - * New upstream version - -BLOCKER: Build tests fail - still. - - -- Steffen Moeller Sat, 12 Sep 2020 03:11:17 +0200 + * Initial release (Closes: #) -pigx-scrnaseq (0.0.8-1) unstable; urgency=medium + BROKEN: - * Initial release (Closes: #) + * Tests fail + * ATM even build-deps are not installable + The following packages have unmet dependencies: + python3-numba : Depends: python3-llvmlite (< 0.35) but 0.35.0-1 is to be installed + E: Unable to correct problems, you have held broken packages. -- Steffen Moeller Tue, 13 Aug 2019 14:49:58 +0200 View it on GitLab: https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/362f491016e0918f990ad7f8a07875e186575c79 -- View it on GitLab: https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/362f491016e0918f990ad7f8a07875e186575c79 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][master] TL;DR for d/TODO
Steffen Möller pushed to branch master at Debian Med / bcbio Commits: a48982aa by Steffen Moeller at 2020-12-13T15:24:43+01:00 TL;DR for d/TODO - - - - - 1 changed file: - debian/TODO Changes: = debian/TODO = @@ -1,6 +1,17 @@ TODO for bcbio with Debian == +TL;DR +- + +We yet fail to run bcbio workflows successfully. The package builds but +tests fail. You get pretty close if installing + * GATK (many Java dependencies not packaged) + * qualimap (sources of Java dependencies no longer available) +manually. However, for the immediate future we suggest to install +bcbio via conda - and cordially invite to help us in bringing bcbio +to Debian. + IF YOU ARE READING THIS AND FEEL LIKE HELPING OUT - PLEASE CONTACT US - View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/a48982aa7bca71129decc931487c09ef30496119 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/a48982aa7bca71129decc931487c09ef30496119 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sepp] Pushed new tag debian/4.3.10+dfsg-4
Steffen Möller pushed new tag debian/4.3.10+dfsg-4 at Debian Med / sepp -- View it on GitLab: https://salsa.debian.org/med-team/sepp/-/tree/debian/4.3.10+dfsg-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sepp][master] Further refinement
Steffen Möller pushed to branch master at Debian Med / sepp Commits: 5fd4cab3 by Steffen Moeller at 2020-12-12T23:29:25+01:00 Further refinement - - - - - 4 changed files: - debian/changelog - debian/control - debian/patches/using_python3_interpreter.patch - debian/rules Changes: = debian/changelog = @@ -1,7 +1,8 @@ -sepp (4.3.10+dfsg-4) UNRELEASED; urgency=medium +sepp (4.3.10+dfsg-4) unstable; urgency=medium * Team upload. * Now truly also bringing d/sepp.install to salsa + * d/rules clean: Allowing for repeated builds cleaning *.jar *.class -- Steffen Moeller Sat, 12 Dec 2020 19:39:54 +0100 = debian/control = @@ -9,12 +9,12 @@ Build-Depends: debhelper-compat (= 13), python3, python3-setuptools, python3-dendropy, - pplacer, - hmmer, ant, libjenkins-json-java, libgoogle-gson-java, - ncbi-blast+ + ncbi-blast+ , + pplacer , + hmmer Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/sepp Vcs-Git: https://salsa.debian.org/med-team/sepp.git = debian/patches/using_python3_interpreter.patch = @@ -5,43 +5,73 @@ Origin: https://www.debian.org/doc/packaging-manuals/python-policy/programs.html Forwarded: https://github.com/smirarab/sepp/issues/88 Last-Update: 2020-10-07 a/run_abundance.py -+++ b/run_abundance.py +Index: sepp/run_abundance.py +=== +--- sepp.orig/run_abundance.py sepp/run_abundance.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- from sepp.metagenomics import main a/run_sepp.py -+++ b/run_sepp.py +Index: sepp/run_sepp.py +=== +--- sepp.orig/run_sepp.py sepp/run_sepp.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- from sepp.exhaustive import ExhaustiveAlgorithm a/run_tipp.py -+++ b/run_tipp.py +Index: sepp/run_tipp.py +=== +--- sepp.orig/run_tipp.py sepp/run_tipp.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- from sepp.exhaustive_tipp import main a/run_tipp_tool.py -+++ b/run_tipp_tool.py +Index: sepp/run_tipp_tool.py +=== +--- sepp.orig/run_tipp_tool.py sepp/run_tipp_tool.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- a/run_upp.py -+++ b/run_upp.py +Index: sepp/run_upp.py +=== +--- sepp.orig/run_upp.py sepp/run_upp.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- from sepp.exhaustive_upp import main +Index: sepp/sepp-package/run-sepp.sh +=== +--- sepp.orig/sepp-package/run-sepp.sh sepp/sepp-package/run-sepp.sh +@@ -134,7 +134,14 @@ set -e + if [ ! -z "$printDebug" ]; then + export SEPP_DEBUG=True + fi; +-python $DIR/sepp/run_sepp.py -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log ++ ++runMe=/usr/bin/run_sepp.py ++if [ -e $DIR/sepp/run_sepp.py ]; then ++ runMe=$DIR/sepp/run_sepp.py ++fi ++ ++echo "I: Invoking python3 $runMe -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log" ++python3 $runMe -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log + + tail sepp-$name-* + = debian/rules = @@ -38,6 +38,10 @@ override_dh_auto_clean: $(RM) -rf tools/bundled $(RM) -rf tools/merge/build $(RM) sepp.config tipp.config upp.config + find . -name "*.class" -delete + find . -name "*.jar" -delete + rm -f home.path sepp.egg-info/PKG-INFO sepp.egg-info/SOURCES.txt sepp.egg-info/dependency_links.txt sepp.egg-info/requires.txt sepp.egg-info/top_level.txt + override_dh_auto_install: dh_auto_install View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/5fd4cab3e7c8a096cb4b631b60916b75eddc0503 -- View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/5fd4cab3e7c8a096cb4b631b60916b75eddc0503 You're receiving this email because of your account on salsa.debian.org
[med-svn] [Git][med-team/q2-fragment-insertion][master] 2 commits: Refinement of d/control
Steffen Möller pushed to branch master at Debian Med / q2-fragment-insertion
Commits:
93e76b75 by Steffen Möller at 2020-12-12T15:04:38+01:00
Refinement of d/control
- - - - -
3ebeb983 by Steffen Möller at 2020-12-13T00:36:37+01:00
runtime test will fail also with run-sepp.sh in place
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/python2to3.patch
- + debian/patches/series
- debian/tests/control
Changes:
=
debian/changelog
=
@@ -1,4 +1,4 @@
-q2-fragment-insertion (2020.11.1-1) unstable; urgency=medium
+q2-fragment-insertion (2020.11.1-1) UNRELEASED; urgency=medium
* Initial release (Closes: #977115)
=
debian/control
=
@@ -7,10 +7,11 @@ Build-Depends: debhelper-compat (= 13),
dh-python,
python3,
python3-setuptools,
- python3-pytest-cov,
- python3-biom-format,
qiime (>= 2020.11.0),
- python3-skbio
+ python3-pytest ,
+ python3-pytest-cov ,
+ python3-biom-format ,
+ python3-skbio
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/q2-fragment-insertion
Vcs-Git: https://salsa.debian.org/med-team/q2-fragment-insertion.git
@@ -26,9 +27,9 @@ Depends: ${shlibs:Depends},
python3-biom-format,
python3-skbio,
q2-types (>= 2020.11.1)
-Recommends: sepp,
+Recommends: sepp (>= 4.3.10+dfsg-4),
python3-ijson,
-default-jdk,
+default-jdk
Description: QIIME 2 plugin for fragment insertion
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
=
debian/patches/python2to3.patch
=
@@ -0,0 +1,17 @@
+Index: q2-fragment-insertion/Makefile
+===
+--- q2-fragment-insertion.orig/Makefile
q2-fragment-insertion/Makefile
+@@ -7,10 +7,10 @@ lint:
+ flake8
+
+ test: all
+- py.test
++ py.test-3
+
+ install: all
+- python setup.py install
++ python3 setup.py install
+
+ dev: all
+ pip install -e .
=
debian/patches/series
=
@@ -0,0 +1 @@
+python2to3.patch
=
debian/tests/control
=
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, python3-pytest-cov
+Depends: @, python3-pytest-cov, sepp (>= 4.3.10+dfsg-4)
Restrictions: allow-stderr
View it on GitLab:
https://salsa.debian.org/med-team/q2-fragment-insertion/-/compare/a6c2f0c615573d67c29a6d8645544915b0cc44c7...3ebeb98372f00eb2ed02fdff991e555b14f9d88c
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-fragment-insertion/-/compare/a6c2f0c615573d67c29a6d8645544915b0cc44c7...3ebeb98372f00eb2ed02fdff991e555b14f9d88c
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[med-svn] [Git][med-team/sepp][master] Added sepp.install that was omitted from -3
Steffen Möller pushed to branch master at Debian Med / sepp Commits: fbee3df9 by Steffen Moeller at 2020-12-12T19:41:35+01:00 Added sepp.install that was omitted from -3 - - - - - 2 changed files: - debian/changelog - + debian/sepp.install Changes: = debian/changelog = @@ -1,3 +1,10 @@ +sepp (4.3.10+dfsg-4) UNRELEASED; urgency=medium + + * Team upload. + * Now truly also bringing d/sepp.install to salsa + + -- Steffen Moeller Sat, 12 Dec 2020 19:39:54 +0100 + sepp (4.3.10+dfsg-3) unstable; urgency=medium * Team upload. = debian/sepp.install = @@ -0,0 +1 @@ +sepp-package/run-sepp.sh usr/bin View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/fbee3df9639742e167a1bbed6bc85ba3c4947276 -- View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/fbee3df9639742e167a1bbed6bc85ba3c4947276 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sepp] Pushed new tag debian/4.3.10+dfsg-3
Steffen Möller pushed new tag debian/4.3.10+dfsg-3 at Debian Med / sepp -- View it on GitLab: https://salsa.debian.org/med-team/sepp/-/tree/debian/4.3.10+dfsg-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sepp][master] Upload of -3
Steffen Möller pushed to branch master at Debian Med / sepp Commits: 8e5b96eb by Steffen Moeller at 2020-12-12T14:57:54+01:00 Upload of -3 - - - - - 2 changed files: - debian/changelog - debian/upstream/metadata Changes: = debian/changelog = @@ -1,4 +1,4 @@ -sepp (4.3.10+dfsg-3) UNRELEASED; urgency=medium +sepp (4.3.10+dfsg-3) unstable; urgency=medium * Team upload. * Also redistributing sepp-package/run-sepp.sh which is expected = debian/upstream/metadata = @@ -3,6 +3,8 @@ Registry: Entry: sepp - Name: bio.tools Entry: NA + - Name; SciCrunch + Entry: NA Bug-Database: https://github.com/smirarab/sepp/issues Bug-Submit: https://github.com/smirarab/sepp/issues/new Repository: https://github.com/smirarab/sepp.git View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/8e5b96ebce8f6cb4587fd0c38db062ffc7ed9b95 -- View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/8e5b96ebce8f6cb4587fd0c38db062ffc7ed9b95 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sepp][master] Also redistributing run-sepp.sh for q2-fragment-insertion
Steffen Möller pushed to branch master at Debian Med / sepp
Commits:
d5602816 by Steffen Moeller at 2020-12-12T01:26:10+01:00
Also redistributing run-sepp.sh for q2-fragment-insertion
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/sepp.lintian-overrides
Changes:
=
debian/changelog
=
@@ -1,3 +1,12 @@
+sepp (4.3.10+dfsg-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Also redistributing sepp-package/run-sepp.sh which is expected
+by q2-fragment-insertion.
+ * Bumped policy-compliance to 4.5.1.
+
+ -- Steffen Moeller Sat, 12 Dec 2020 01:20:51 +0100
+
sepp (4.3.10+dfsg-2) unstable; urgency=medium
* Remove trailing whitespace in debian/rules (routine-update)
=
debian/control
=
@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13),
libjenkins-json-java,
libgoogle-gson-java,
ncbi-blast+
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/sepp
Vcs-Git: https://salsa.debian.org/med-team/sepp.git
Homepage: https://github.com/smirarab/sepp/
@@ -36,7 +36,7 @@ Depends: ${shlibs:Depends},
libcommons-lang-java,
libcommons-logging-java,
ncbi-blast+
-Description: methods use ensembles of Hidden Markov Models (HMM)
+Description: phylogeny with ensembles of Hidden Markov Models
The tools SEPP and TIPP implementing these methods use ensembles of Hidden
Markov Models (HMMs) in different ways, each focusing on a different problem.
.
=
debian/sepp.lintian-overrides
=
@@ -1,2 +1,4 @@
# see https://lists.debian.org/debian-med/2018/06/msg00043.html
script-with-language-extension usr/bin/*.py
+# The .sh one has a reverse dependency in q2-fragment-insertion
+script-with-language-extension usr/bin/*.sh
View it on GitLab:
https://salsa.debian.org/med-team/sepp/-/commit/d5602816a20c49d02100f2b60642a70e6603c26f
--
View it on GitLab:
https://salsa.debian.org/med-team/sepp/-/commit/d5602816a20c49d02100f2b60642a70e6603c26f
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[med-svn] [Git][med-team/q2-fragment-insertion][master] Added helper script, added runtim deps
Steffen Möller pushed to branch master at Debian Med / q2-fragment-insertion
Commits:
8281fea2 by Steffen Möller at 2020-12-11T01:36:33+01:00
Added helper script, added runtim deps
- - - - -
3 changed files:
- debian/control
- + debian/q2-fragment-insertion.dirs
- + debian/q2-fragment-insertion.install
Changes:
=
debian/control
=
@@ -23,6 +23,10 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
qiime (>= 2020.11.0)
+Recommends: sepp,
+python3-ijson,
+default-jdk,
+q2-types (>= 2020.11.1)
Description: QIIME 2 plugin for fragment insertion
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
=
debian/q2-fragment-insertion.dirs
=
@@ -0,0 +1 @@
+usr/share/q2-fragment-insertion
=
debian/q2-fragment-insertion.install
=
@@ -0,0 +1 @@
+bin/* usr/share/q2-fragment-insertion/
View it on GitLab:
https://salsa.debian.org/med-team/q2-fragment-insertion/-/commit/8281fea22d641e7ba78611dc9f19d4dc079bcc36
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-fragment-insertion/-/commit/8281fea22d641e7ba78611dc9f19d4dc079bcc36
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[med-svn] [Git][med-team/q2-dada2][master] Update control - extended description.
Steffen Möller pushed to branch master at Debian Med / q2-dada2 Commits: a20f2431 by Steffen Möller at 2020-12-08T23:49:25+00:00 Update control - extended description. - - - - - 1 changed file: - debian/control Changes: = debian/control = @@ -44,3 +44,7 @@ Description: QIIME 2 plugin to work with adapters in sequence data can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed. + . + This package wraps the dada2 R package in BioConductor for modeling and + correcting Illumina-sequenced amplicon errors. This was shown to improve the + sensitivity of diversity analyses. \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/q2-dada2/-/commit/a20f2431284f9b4e9ab30af425beeabfc8fa6604 -- View it on GitLab: https://salsa.debian.org/med-team/q2-dada2/-/commit/a20f2431284f9b4e9ab30af425beeabfc8fa6604 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-cutadapt] Pushed new tag debian/2020.11.1-1
Steffen Möller pushed new tag debian/2020.11.1-1 at Debian Med / q2-cutadapt -- View it on GitLab: https://salsa.debian.org/med-team/q2-cutadapt/-/tree/debian/2020.11.1-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-cutadapt] Pushed new tag upstream/2020.11.1
Steffen Möller pushed new tag upstream/2020.11.1 at Debian Med / q2-cutadapt -- View it on GitLab: https://salsa.debian.org/med-team/q2-cutadapt/-/tree/upstream/2020.11.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-cutadapt][upstream] New upstream version 2020.11.1
Steffen Möller pushed to branch upstream at Debian Med / q2-cutadapt
Commits:
96109dc2 by Steffen Moeller at 2020-12-08T18:32:19+01:00
New upstream version 2020.11.1
- - - - -
1 changed file:
- q2_cutadapt/_version.py
Changes:
=
q2_cutadapt/_version.py
=
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
-git_refnames = " (HEAD -> master, tag: 2020.11.0)"
-git_full = "8a18174db6b284af087f8bc82b0b717a446aab4e"
-git_date = "2020-11-25 17:13:09 +"
+git_refnames = " (HEAD -> master, tag: 2020.11.1)"
+git_full = "13b69a6fd0be98d8d089cec05612466765dcb0de"
+git_date = "2020-12-05 20:44:46 +"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab:
https://salsa.debian.org/med-team/q2-cutadapt/-/commit/96109dc2d1ba7db56549287a2f9f698dc3139d94
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-cutadapt/-/commit/96109dc2d1ba7db56549287a2f9f698dc3139d94
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[med-svn] [Git][med-team/q2-cutadapt][master] 6 commits: New upstream version 2020.11.1
Steffen Möller pushed to branch master at Debian Med / q2-cutadapt
Commits:
96109dc2 by Steffen Moeller at 2020-12-08T18:32:19+01:00
New upstream version 2020.11.1
- - - - -
173c4df3 by Steffen Moeller at 2020-12-08T18:32:19+01:00
routine-update: New upstream version
- - - - -
611ee985 by Steffen Moeller at 2020-12-08T18:32:23+01:00
Update upstream source from tag upstream/2020.11.1
Update to upstream version 2020.11.1
with Debian dir b164f2ba0e7870520f989377e42c736b37f374d6
- - - - -
eff2edd9 by Steffen Moeller at 2020-12-08T18:32:26+01:00
routine-update: Remove trailing whitespace in debian/rules
- - - - -
cee296ff by Steffen Moeller at 2020-12-08T18:32:27+01:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
fe4d50ff by Steffen Moeller at 2020-12-08T18:35:53+01:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/rules
- debian/upstream/metadata
- q2_cutadapt/_version.py
Changes:
=
debian/changelog
=
@@ -1,3 +1,12 @@
+q2-cutadapt (2020.11.1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Remove trailing whitespace in debian/rules (routine-update)
+ * d/u/metadata: add refs to registries
+
+ -- Steffen Moeller Tue, 08 Dec 2020 18:32:29 +0100
+
q2-cutadapt (2020.11.0-1) unstable; urgency=medium
* Team upload.
=
debian/rules
=
@@ -13,7 +13,7 @@ export PYBUILD_AFTER_TEST=rm -v {build_dir}/site.py
{build_dir}/.coverage*; \
%:
dh $@ --with python3 --buildsystem=pybuild
-# FIXME: similarly to the qiime and q2-types packages, the build time testing
fails, as
+# FIXME: similarly to the qiime and q2-types packages, the build time testing
fails, as
#the Qiime plugin system is not fully available at this point of the
package
#construction. The test suite is only run at autopkgtest time, but
this
#is not ideal, since the only tested python version is the default one.
@@ -25,4 +25,3 @@ endif
override_dh_auto_clean:
dh_auto_clean
rm -f q2_cutadapt.egg-info/PKG-INFO q2_cutadapt.egg-info/SOURCES.txt
q2_cutadapt.egg-info/dependency_links.txt q2_cutadapt.egg-info/entry_points.txt
q2_cutadapt.egg-info/not-zip-safe q2_cutadapt.egg-info/top_level.txt
-
=
debian/upstream/metadata
=
@@ -46,3 +46,8 @@ Reference:
eprint: https://www.nature.com/articles/s41587-019-0209-9.pdf
Repository: https://github.com/qiime2/q2-cutadapt.git
Repository-Browse: https://github.com/qiime2/q2-cutadapt
+Registry:
+ - Name: bio.tools
+ Entry: NA
+ - Name: conda:qiime2
+ Entry: q2-cutadapt
=
q2_cutadapt/_version.py
=
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
-git_refnames = " (HEAD -> master, tag: 2020.11.0)"
-git_full = "8a18174db6b284af087f8bc82b0b717a446aab4e"
-git_date = "2020-11-25 17:13:09 +"
+git_refnames = " (HEAD -> master, tag: 2020.11.1)"
+git_full = "13b69a6fd0be98d8d089cec05612466765dcb0de"
+git_date = "2020-12-05 20:44:46 +"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab:
https://salsa.debian.org/med-team/q2-cutadapt/-/compare/16dc7b27bfed6fea2e2d421edf0bb0b3ef33a1b1...fe4d50ff836f6570ca6b599348a3858322a7c8fd
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-cutadapt/-/compare/16dc7b27bfed6fea2e2d421edf0bb0b3ef33a1b1...fe4d50ff836f6570ca6b599348a3858322a7c8fd
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[med-svn] [Git][med-team/q2-cutadapt][pristine-tar] pristine-tar data for q2-cutadapt_2020.11.1.orig.tar.gz
Steffen Möller pushed to branch pristine-tar at Debian Med / q2-cutadapt Commits: 9db9f31d by Steffen Moeller at 2020-12-08T18:32:23+01:00 pristine-tar data for q2-cutadapt_2020.11.1.orig.tar.gz - - - - - 2 changed files: - + q2-cutadapt_2020.11.1.orig.tar.gz.delta - + q2-cutadapt_2020.11.1.orig.tar.gz.id Changes: = q2-cutadapt_2020.11.1.orig.tar.gz.delta = Binary files /dev/null and b/q2-cutadapt_2020.11.1.orig.tar.gz.delta differ = q2-cutadapt_2020.11.1.orig.tar.gz.id = @@ -0,0 +1 @@ +1990e00808aeed044d323431d51dddb1ea86f4b2 View it on GitLab: https://salsa.debian.org/med-team/q2-cutadapt/-/commit/9db9f31d083dd771db43d6371e4e977c6282472a -- View it on GitLab: https://salsa.debian.org/med-team/q2-cutadapt/-/commit/9db9f31d083dd771db43d6371e4e977c6282472a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/trimmomatic][master] Update metadata - update bio.tools
Steffen Möller pushed to branch master at Debian Med / trimmomatic Commits: ebc8e28e by Steffen Möller at 2020-12-07T23:31:35+00:00 Update metadata - update bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -17,6 +17,6 @@ Registry: - Name: SciCrunch Entry: SCR_011848 - Name: bio.tools - Entry: Trimmomatic + Entry: trimmomatic - Name: conda:bioconda Entry: trimmomatic View it on GitLab: https://salsa.debian.org/med-team/trimmomatic/-/commit/ebc8e28eea2fb132c9807d1735ad3d134c5bb388 -- View it on GitLab: https://salsa.debian.org/med-team/trimmomatic/-/commit/ebc8e28eea2fb132c9807d1735ad3d134c5bb388 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-demux][pristine-tar] pristine-tar data for q2-demux_2020.11.1.orig.tar.gz
Steffen Möller pushed to branch pristine-tar at Debian Med / q2-demux Commits: ebe03392 by Steffen Moeller at 2020-12-07T23:02:21+01:00 pristine-tar data for q2-demux_2020.11.1.orig.tar.gz - - - - - 2 changed files: - + q2-demux_2020.11.1.orig.tar.gz.delta - + q2-demux_2020.11.1.orig.tar.gz.id Changes: = q2-demux_2020.11.1.orig.tar.gz.delta = Binary files /dev/null and b/q2-demux_2020.11.1.orig.tar.gz.delta differ = q2-demux_2020.11.1.orig.tar.gz.id = @@ -0,0 +1 @@ +3cae112e938bc249923642359d1a197ab0f661a5 View it on GitLab: https://salsa.debian.org/med-team/q2-demux/-/commit/ebe03392aa051245acf4a7ddbaeba79c6da64ae7 -- View it on GitLab: https://salsa.debian.org/med-team/q2-demux/-/commit/ebe03392aa051245acf4a7ddbaeba79c6da64ae7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-demux] Pushed new tag upstream/2020.11.1
Steffen Möller pushed new tag upstream/2020.11.1 at Debian Med / q2-demux -- View it on GitLab: https://salsa.debian.org/med-team/q2-demux/-/tree/upstream/2020.11.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-demux] Pushed new tag debian/2020.11.1-1
Steffen Möller pushed new tag debian/2020.11.1-1 at Debian Med / q2-demux -- View it on GitLab: https://salsa.debian.org/med-team/q2-demux/-/tree/debian/2020.11.1-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/q2-demux][upstream] New upstream version 2020.11.1
Steffen Möller pushed to branch upstream at Debian Med / q2-demux
Commits:
509048dd by Steffen Moeller at 2020-12-07T23:02:20+01:00
New upstream version 2020.11.1
- - - - -
4 changed files:
- .gitignore
- Makefile
- − q2_demux/_summarize/assets/package-lock.json
- q2_demux/_version.py
Changes:
=
.gitignore
=
@@ -72,3 +72,4 @@ target/
.DS_Store
node_modules
+package-lock.json
=
Makefile
=
@@ -16,7 +16,7 @@ test-cov: all
q2_demux/_summarize/assets/dist:
cd q2_demux/_summarize/assets && \
- npm install && \
+ npm install --no-save && \
npm run build && \
cp licenses/* dist/
=
q2_demux/_summarize/assets/package-lock.json deleted
=
The diff for this file was not included because it is too large.
=
q2_demux/_version.py
=
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
-git_refnames = " (HEAD -> master, tag: 2020.11.0)"
-git_full = "3d775a03bb152c30b2b0fd57b5f44a4c1d2f4273"
-git_date = "2020-11-25 17:13:07 +"
+git_refnames = " (HEAD -> master, tag: 2020.11.1)"
+git_full = "5769fc493a3a6479b2d648151fb1a10c8b1426fd"
+git_date = "2020-12-05 20:44:49 +"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab:
https://salsa.debian.org/med-team/q2-demux/-/commit/509048dd2bf836eced94ac442dd7bb702f7bd676
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-demux/-/commit/509048dd2bf836eced94ac442dd7bb702f7bd676
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[med-svn] [Git][med-team/q2-demux][master] 5 commits: New upstream version 2020.11.1
Steffen Möller pushed to branch master at Debian Med / q2-demux
Commits:
509048dd by Steffen Moeller at 2020-12-07T23:02:20+01:00
New upstream version 2020.11.1
- - - - -
df9d1f7b by Steffen Moeller at 2020-12-07T23:02:20+01:00
routine-update: New upstream version
- - - - -
285fcffd by Steffen Moeller at 2020-12-07T23:02:21+01:00
Update upstream source from tag upstream/2020.11.1
Update to upstream version 2020.11.1
with Debian dir d1d035c1fd33d5ade8c4a994c58e7fd72d546502
- - - - -
a3941b69 by Steffen Moeller at 2020-12-07T23:02:23+01:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
9a1828ad by Steffen Moeller at 2020-12-07T23:02:53+01:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- .gitignore
- Makefile
- debian/changelog
- debian/rules
- − q2_demux/_summarize/assets/package-lock.json
- q2_demux/_version.py
Changes:
=
.gitignore
=
@@ -72,3 +72,4 @@ target/
.DS_Store
node_modules
+package-lock.json
=
Makefile
=
@@ -16,7 +16,7 @@ test-cov: all
q2_demux/_summarize/assets/dist:
cd q2_demux/_summarize/assets && \
- npm install && \
+ npm install --no-save && \
npm run build && \
cp licenses/* dist/
=
debian/changelog
=
@@ -1,3 +1,10 @@
+q2-demux (2020.11.1-1) unstable; urgency=medium
+
+ * New upstream version
+ * Trim trailing whitespace.
+
+ -- Steffen Moeller Mon, 07 Dec 2020 23:02:24 +0100
+
q2-demux (2020.11.0-1) unstable; urgency=medium
* New upstream version
=
debian/rules
=
@@ -24,4 +24,3 @@ endif
override_dh_auto_clean:
dh_auto_clean
rm -f q2_demux.egg-info/PKG-INFO q2_demux.egg-info/SOURCES.txt
q2_demux.egg-info/dependency_links.txt q2_demux.egg-info/entry_points.txt
q2_demux.egg-info/not-zip-safe q2_demux.egg-info/top_level.txt
-
=
q2_demux/_summarize/assets/package-lock.json deleted
=
The diff for this file was not included because it is too large.
=
q2_demux/_version.py
=
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
-git_refnames = " (HEAD -> master, tag: 2020.11.0)"
-git_full = "3d775a03bb152c30b2b0fd57b5f44a4c1d2f4273"
-git_date = "2020-11-25 17:13:07 +"
+git_refnames = " (HEAD -> master, tag: 2020.11.1)"
+git_full = "5769fc493a3a6479b2d648151fb1a10c8b1426fd"
+git_date = "2020-12-05 20:44:49 +"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab:
https://salsa.debian.org/med-team/q2-demux/-/compare/b70e5adcd107ff2333aa3d58a4a23978d0be9a8f...9a1828adf7b9de81a76f9fb0191e904d4b3aa951
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-demux/-/compare/b70e5adcd107ff2333aa3d58a4a23978d0be9a8f...9a1828adf7b9de81a76f9fb0191e904d4b3aa951
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[med-svn] [Git][med-team/bcbio][master] 2 commits: Extended paths available for testing
Steffen Möller pushed to branch master at Debian Med / bcbio Commits: a2aa99d1 by Steffen Moeller at 2020-12-07T18:40:02+01:00 Extended paths available for testing - - - - - 097a6fd6 by Steffen Moeller at 2020-12-07T18:40:30+01:00 Added build dependencies - - - - - 2 changed files: - debian/control - debian/patches/pythonpaths.patch Changes: = debian/control = @@ -57,7 +57,9 @@ Build-Depends: debhelper-compat (= 13), r-other-wasabi , r-bioc-htsfilter , r-bioc-degreport , + r-bioc-purecn , r-cran-tidyverse , + r-bioc-titancna , r-bioc-tximport , r-other-wasabi , salmon , @@ -112,6 +114,8 @@ Recommends: python3-statsmodels, python3-tabulate, r-other-wasabi, + r-bioc-purecn, + r-bioc-titancna, seqan-apps, vcfanno, vt = debian/patches/pythonpaths.patch = @@ -67,7 +67,7 @@ Index: bcbio/tests/run_tests.sh unset PYTHONHOME -unset PYTHONPATH -+export PATH=$(pwd)/scripts:$PATH ++export PATH=$(pwd)/scripts:/usr/lib/debian-med/bin:$PATH +export PYTHONPATH=$(pwd) export PYTHONNOUSERSITE=1 # Ensure version.py exists in raw cloned bcbio directory View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/d94cceaa36d209359b470b29278d2fac746f2901...097a6fd6f3b31b588aa034a942d480a124352aaa -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/d94cceaa36d209359b470b29278d2fac746f2901...097a6fd6f3b31b588aa034a942d480a124352aaa You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mafft] Pushed new tag upstream/7.475
Steffen Möller pushed new tag upstream/7.475 at Debian Med / mafft -- View it on GitLab: https://salsa.debian.org/med-team/mafft/-/tree/upstream/7.475 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mafft] Pushed new tag debian/7.475-1
Steffen Möller pushed new tag debian/7.475-1 at Debian Med / mafft -- View it on GitLab: https://salsa.debian.org/med-team/mafft/-/tree/debian/7.475-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mafft][pristine-tar] pristine-tar data for mafft_7.475.orig.tar.gz
Steffen Möller pushed to branch pristine-tar at Debian Med / mafft Commits: 8eb52f78 by Steffen Moeller at 2020-12-07T18:22:14+01:00 pristine-tar data for mafft_7.475.orig.tar.gz - - - - - 2 changed files: - + mafft_7.475.orig.tar.gz.delta - + mafft_7.475.orig.tar.gz.id Changes: = mafft_7.475.orig.tar.gz.delta = Binary files /dev/null and b/mafft_7.475.orig.tar.gz.delta differ = mafft_7.475.orig.tar.gz.id = @@ -0,0 +1 @@ +a741f58555d2b3163eb60c104d95137d8eb4eb47 View it on GitLab: https://salsa.debian.org/med-team/mafft/-/commit/8eb52f78b631fd92fe8787cb7697fc38a0e0a595 -- View it on GitLab: https://salsa.debian.org/med-team/mafft/-/commit/8eb52f78b631fd92fe8787cb7697fc38a0e0a595 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pbcommand] Pushed new tag upstream/2.1.1+git20201023.cc0ed3d
Steffen Möller pushed new tag upstream/2.1.1+git20201023.cc0ed3d at Debian Med / python-pbcommand -- View it on GitLab: https://salsa.debian.org/med-team/python-pbcommand/-/tree/upstream/2.1.1+git20201023.cc0ed3d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pbcommand] Pushed new tag upstream/1.1.1+git20201023.cc0ed3d
Steffen Möller pushed new tag upstream/1.1.1+git20201023.cc0ed3d at Debian Med / python-pbcommand -- View it on GitLab: https://salsa.debian.org/med-team/python-pbcommand/-/tree/upstream/1.1.1+git20201023.cc0ed3d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pbcommand] Pushed new tag debian/2.1.1+git20201023.cc0ed3d-1
Steffen Möller pushed new tag debian/2.1.1+git20201023.cc0ed3d-1 at Debian Med / python-pbcommand -- View it on GitLab: https://salsa.debian.org/med-team/python-pbcommand/-/tree/debian/2.1.1+git20201023.cc0ed3d-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pbcommand][pristine-tar] 2 commits: pristine-tar data for python-pbcommand_1.1.1+git20201023.cc0ed3d.orig.tar.xz
Steffen Möller pushed to branch pristine-tar at Debian Med / python-pbcommand Commits: 70dde775 by Steffen Moeller at 2020-12-07T16:24:19+01:00 pristine-tar data for python-pbcommand_1.1.1+git20201023.cc0ed3d.orig.tar.xz - - - - - 53d36540 by Steffen Moeller at 2020-12-07T16:42:02+01:00 pristine-tar data for python-pbcommand_2.1.1+git20201023.cc0ed3d.orig.tar.xz - - - - - 4 changed files: - + python-pbcommand_1.1.1+git20201023.cc0ed3d.orig.tar.xz.delta - + python-pbcommand_1.1.1+git20201023.cc0ed3d.orig.tar.xz.id - + python-pbcommand_2.1.1+git20201023.cc0ed3d.orig.tar.xz.delta - + python-pbcommand_2.1.1+git20201023.cc0ed3d.orig.tar.xz.id Changes: = python-pbcommand_1.1.1+git20201023.cc0ed3d.orig.tar.xz.delta = Binary files /dev/null and b/python-pbcommand_1.1.1+git20201023.cc0ed3d.orig.tar.xz.delta differ = python-pbcommand_1.1.1+git20201023.cc0ed3d.orig.tar.xz.id = @@ -0,0 +1 @@ +1ba72455280993f7201899ff272705908d145197 = python-pbcommand_2.1.1+git20201023.cc0ed3d.orig.tar.xz.delta = Binary files /dev/null and b/python-pbcommand_2.1.1+git20201023.cc0ed3d.orig.tar.xz.delta differ = python-pbcommand_2.1.1+git20201023.cc0ed3d.orig.tar.xz.id = @@ -0,0 +1 @@ +1ba72455280993f7201899ff272705908d145197 View it on GitLab: https://salsa.debian.org/med-team/python-pbcommand/-/compare/f21d520660a6fd8d61b7843b96de73259c3ce4e3...53d365407f7b0c345e8dda5b707fae83db0c7725 -- View it on GitLab: https://salsa.debian.org/med-team/python-pbcommand/-/compare/f21d520660a6fd8d61b7843b96de73259c3ce4e3...53d365407f7b0c345e8dda5b707fae83db0c7725 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/signalalign][master] Update metadata - added ref to bio.tools
Steffen Möller pushed to branch master at Debian Med / signalalign Commits: 9ae08180 by Steffen Möller at 2020-12-06T17:18:51+00:00 Update metadata - added ref to bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,3 +1,7 @@ Registry: - Name: conda:bioconda Entry: NA + - Name: bio.tools +Entry: signalalign + - Name: SciCrunch +Entry: NA View it on GitLab: https://salsa.debian.org/med-team/signalalign/-/commit/9ae08180951ca0841f1e460ae0c7e6852749f6d7 -- View it on GitLab: https://salsa.debian.org/med-team/signalalign/-/commit/9ae08180951ca0841f1e460ae0c7e6852749f6d7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/muscle][master] Update metadata - update d/u/metadata bio.tools
Steffen Möller pushed to branch master at Debian Med / muscle Commits: c4e2ef14 by Steffen Möller at 2020-12-06T15:29:52+00:00 Update metadata - update d/u/metadata bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -28,7 +28,7 @@ Registry: - Name: OMICtools Entry: OMICS_00982 - Name: bio.tools - Entry: MUSCLE + Entry: muscle - Name: SciCrunch Entry: SCR_011812 - Name: conda:bioconda View it on GitLab: https://salsa.debian.org/med-team/muscle/-/commit/c4e2ef14496f8f238e532dd4c1b0434339baaac8 -- View it on GitLab: https://salsa.debian.org/med-team/muscle/-/commit/c4e2ef14496f8f238e532dd4c1b0434339baaac8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-gffutils][master] Update metadata - update of bio.tools
Steffen Möller pushed to branch master at Debian Med / python-gffutils Commits: d8a7e7a0 by Steffen Möller at 2020-12-05T15:08:15+00:00 Update metadata - update of bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -6,7 +6,7 @@ Registry: - Name: SciCrunch Entry: NA - Name: bio.tools - Entry: GFFutils + Entry: gffutils - Name: conda:bioconda Entry: gffutils Repository: https://github.com/daler/gffutils.git View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/-/commit/d8a7e7a0fd1e557c630887c6201931f7dfb8f1c3 -- View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/-/commit/d8a7e7a0fd1e557c630887c6201931f7dfb8f1c3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
