[Blends-commit] [Git][blends-team/med][master] 3 commits: Add new packages
Andreas Tille
gitlab at salsa.debian.org
Wed Jun 17 08:47:49 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
30ae50d9 by Andreas Tille at 2020-06-16T19:48:07+02:00
Add new packages
- - - - -
e744c43b by Andreas Tille at 2020-06-17T08:08:04+02:00
Add nanofilt
- - - - -
b9703b20 by Andreas Tille at 2020-06-17T09:47:12+02:00
Fix query to avoid duplicates and update to latest status of UDD
- - - - -
4 changed files:
- covid-19_doc/bio_covid-19_dependencies_query
- covid-19_doc/bio_covid-19_dependencies_result
- tasks/bio
- tasks/covid-19
Changes:
=====================================
covid-19_doc/bio_covid-19_dependencies_query
=====================================
@@ -210,6 +210,7 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'rna-star'),
(DEFAULT,'streamformatics'),
(DEFAULT,'strelka'),
+(DEFAULT,'streamz'),
(DEFAULT,'tiddit'),
(DEFAULT,'tombo'),
(DEFAULT,'tophat-recondition'),
@@ -286,7 +287,9 @@ SELECT co.package, architectures, s.section,
JOIN (SELECT DISTINCT source, package FROM packages WHERE release in ('sid')) p ON r.source = p.source
WHERE name = 'bio.tools') tmp) bt ON bt.package = co.package
LEFT OUTER JOIN (SELECT DISTINCT p.package, p.source, s.testsuite FROM packages p
- LEFT JOIN (SELECT source, testsuite FROM sources WHERE release = 'sid') s ON p.source = s.source ) t ON co.package = t.package
+ LEFT JOIN (SELECT source, testsuite FROM -- avoid duplicates when having instances with and without testsuite for different architectures
+ (SELECT source, testsuite, row_number() OVER (PARTITION BY source ORDER BY testsuite) FROM sources WHERE release = 'sid' ) tmp
+ WHERE row_number= 1) s ON p.source = s.source ) t ON co.package = t.package
ORDER BY id
;
END;
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Mon, 15 Jun 2020 09:01:52 +0200
+Last-Update: Wed, 17 Jun 2020 09:43:18 +0200
package | architectures | section | releases | conda | bio.tools | testsuite
------------------------+---------------------+----------+-----------------------------------------------------+----------------------+---------------+-------------------------------------
@@ -13,7 +13,7 @@ Last-Update: Mon, 15 Jun 2020 09:01:52 +0200
smartseq2 | | | | | |
viralcon | | | | | |
nf-core | | | | | |
- abacas | all | main | buster,bullseye,sid | | |
+ abacas | all | main | buster,bullseye,sid | | | autopkgtest
allelecount | amd64,arm64,ppc64el | main | bullseye,sid | cancerit-allelecount | | autopkgtest-pkg-perl
python3-anndata | | | new | anndata | |
libargs-dev | | | new | | |
@@ -23,7 +23,7 @@ Last-Update: Mon, 15 Jun 2020 09:01:52 +0200
libatomicbitvector-dev | all | main | bullseye,sid | | | autopkgtest
augustus | amd64,arm64,ppc64el | main | buster,bullseye,sid | augustus | AUGUSTUS | autopkgtest
bandage | amd64,arm64,ppc64el | main | buster,bullseye,sid | bandage | bandage |
- libbbhash-dev | | | new | | |
+ libbbhash-dev | amd64,arm64,ppc64el | main | sid | | | autopkgtest
bcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid | bcftools | bcftools | autopkgtest
bedtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | biotools | bedtools | autopkgtest
python3-biopython | amd64,arm64,ppc64el | main | buster,bullseye,sid | | Biopython | autopkgtest
@@ -35,7 +35,7 @@ Last-Update: Mon, 15 Jun 2020 09:01:52 +0200
cat-bat | amd64,arm64,ppc64el | main | bullseye,sid | cat | |
centrifuge | amd64 | main | buster,bullseye,sid | centrifuge | Centrifuge |
changeo | all | main | buster,bullseye,sid | changeo | | autopkgtest-pkg-python
- python3-cooler | | | | | |
+ python3-cooler | | | https://salsa.debian.org/med-team/python-cooler | cooler | |
cutadapt | all | main | buster,bullseye,sid | cutadapt | cutadapt | autopkgtest-pkg-python
diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid | diamond | Diamond | autopkgtest
python3-deeptools | all | main | bullseye,sid | deeptools | deeptools | autopkgtest, autopkgtest-pkg-python
@@ -84,7 +84,7 @@ Last-Update: Mon, 15 Jun 2020 09:01:52 +0200
muscle | amd64,arm64,ppc64el | main | buster,bullseye,sid | muscle | MUSCLE | autopkgtest
nanofilt | | | | | |
nanolyse | | | https://salsa.debian.org/med-team/nanolyse | nanolyse | |
- python3-nanomath | all | main | sid | | | autopkgtest
+ python3-nanomath | all | main | bullseye,sid | | | autopkgtest
nanopolish | amd64,arm64 | main | buster,bullseye,sid | nanopolish | nanopolish | autopkgtest
nanook | all | main | buster,bullseye,sid | | NanoOK |
nanoraw | | | | | |
@@ -136,6 +136,7 @@ Last-Update: Mon, 15 Jun 2020 09:01:52 +0200
seqkit | | | | | |
seqtk | amd64,arm64,ppc64el | main | buster,bullseye,sid | seqtk | seqtk | autopkgtest
seqwish | | | https://salsa.debian.org/med-team/seqwish | seqwish | |
+ signalalign | | | | | |
skesa | amd64 | main | bullseye,sid | skesa | |
snpeff | | | https://salsa.debian.org/med-team/snpeff | snpeff | |
snpsift | | | https://salsa.debian.org/med-team/snpeff | snpeff | |
@@ -144,6 +145,7 @@ Last-Update: Mon, 15 Jun 2020 09:01:52 +0200
rna-star | amd64,arm64,ppc64el | main | buster,bullseye,sid | star | star | autopkgtest
streamformatics | | | | | |
strelka | | | https://salsa.debian.org/med-team/strelka | strelka | |
+ streamz | | | | | |
tiddit | | | new | tiddit | |
tombo | | | | | |
tophat-recondition | all | main | bullseye,sid | | |
@@ -169,5 +171,5 @@ Last-Update: Mon, 15 Jun 2020 09:01:52 +0200
python3-pandas | all | main | buster,bullseye,sid | | | autopkgtest
python3-toolz | all | main | buster,bullseye,sid | | | autopkgtest
python3-tornado | amd64,arm64,ppc64el | main | buster,bullseye,sid | | | autopkgtest
-(168 Zeilen)
+(169 Zeilen)
=====================================
tasks/bio
=====================================
@@ -862,6 +862,8 @@ Recommends: nanopolish
Suggests: nanolyse
+Recommends: nanofilt
+
Suggests: nanoplot
Suggests: nanosv
@@ -1223,6 +1225,8 @@ Recommends: sap
Remark: Precondition for T-Coffee
see http://wiki.debian.org/DebianMed/TCoffee
+Recommends: scrappie
+
Suggests: scrm
Suggests: seer
@@ -1258,6 +1262,8 @@ Suggests: seqwish
Suggets: sga
+Recommends: shovill
+
Suggests: sibelia
Recommends: signalalign
@@ -1279,8 +1285,6 @@ Remark: This can be regarded as successor of ssaha2
Recommends: smithwaterman
-Recommends: ssw-align
-
Recommends: smrtanalysis
Recommends: snpeff
@@ -1316,6 +1320,8 @@ Remark: Successor for ssaha2 available: smalt
Recommends: sspace
+Recommends: ssw-align
+
Recommends: staden
Recommends: stacks
@@ -1325,6 +1331,8 @@ Language: Java
Suggests: strelka
+Recommends: streamz
+
Recommends: stringtie
Recommends: subread
@@ -1410,6 +1418,8 @@ Recommends: vsearch
Recommends: yaha
+Recommends: yanosim
+
Recommends: canu
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
=====================================
tasks/covid-19
=====================================
@@ -274,12 +274,18 @@ Recommends: python3-seqcluster
Recommends: seqkit
+Recommends: shovill
+
+Recommends: streamz
+
Recommends: tophat-recondition
Recommends: vienna-rna
Recommends: python3-toolz, python3-tornado
+Recommends: yanosim
+
X-Comment: </Jun_Aruga>
X-Comment: TODO: Check out
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/407c6e7587a18c9fd7be6f4ed69a26b2786ce563...b9703b20c5919b0e66666bca99ab3b45d5535e4e
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/407c6e7587a18c9fd7be6f4ed69a26b2786ce563...b9703b20c5919b0e66666bca99ab3b45d5535e4e
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/blends-commit/attachments/20200617/0dfc3a09/attachment-0001.html>
More information about the Blends-commit
mailing list