Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
b746148a by Andreas Tille at 2020-05-24T19:38:47+02:00
Add quicktree
- - - - -
d670336f by Andreas Tille at 2020-05-24T19:38:47+02:00
Find conda ids also in packages in new
- - - - -
0c9c2827 by Andreas Tille at 2020-05-24T19:38:47+02:00
Find conda ids also in packages in blends prospective packages
- - - - -
3 changed files:
- covid-19_doc/bio_covid-19_dependencies_query
- covid-19_doc/bio_covid-19_dependencies_result
- tasks/covid-19
Changes:
=====================================
covid-19_doc/bio_covid-19_dependencies_query
=====================================
@@ -195,7 +195,14 @@ SELECT co.package, architectures, s.section,
LEFT JOIN (SELECT package, vcs_browser FROM blends_prospectivepackages) vcs
ON vcs.package = co.package
LEFT JOIN (SELECT DISTINCT package, entry AS conda FROM (
SELECT p.source, p.package, entry FROM registry r
- JOIN (SELECT DISTINCT source, package FROM packages WHERE
release in ('sid')) p ON r.source = p.source
+ JOIN (SELECT DISTINCT * FROM (
+ SELECT source, package FROM packages WHERE release in
('sid')
+ UNION
+ SELECT source, package FROM new_packages
+ UNION
+ SELECT source, package FROM blends_prospectivepackages
+ ) pkgs
+ ) p ON r.source = p.source
WHERE name = 'conda:bioconda') tmp) conda ON conda.package =
co.package
LEFT JOIN (SELECT DISTINCT package, entry AS biotools FROM (
SELECT p.source, p.package, entry FROM registry r
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Sun, 24 May 2020 10:42:41 +0200
+Last-Update: Sun, 24 May 2020 19:37:02 +0200
package | architectures | section |
releases | conda | bio.tools
-----------------------------+---------------------+----------+---------------------------------------------+--------------------------+--------------
@@ -11,24 +11,24 @@ Last-Update: Sun, 24 May 2020 10:42:41 +0200
busco | all | main | bullseye,sid
| busco |
bustools | amd64,arm64,ppc64el | main | bullseye,sid
| bustools | BUStools
bwa | amd64,arm64,ppc64el | main |
buster,bullseye,sid | bwa | BWA
- cat-bat | | | new
| |
+ cat-bat | | | new
| cat |
centrifuge | amd64 | main |
buster,bullseye,sid | centrifuge |
Centrifuge
changeo | all | main |
buster,bullseye,sid | changeo |
cutadapt | all | main |
buster,bullseye,sid | cutadapt |
cutadapt
diamond-aligner | amd64,arm64,ppc64el | main |
buster,bullseye,sid | diamond | Diamond
- drop-seq-tools | | | new
| |
+ drop-seq-tools | | | new
| dropseq_tools |
fastp | amd64,arm64,ppc64el | main |
buster,bullseye,sid | fastp |
fastqc | all | main |
buster,bullseye,sid | fastqc | FastQC
filtlong | amd64,arm64,ppc64el | main | bullseye,sid
| filtlong |
freebayes | amd64,arm64,ppc64el | main |
buster,bullseye,sid | freebayes |
freebayes
gatk | | |
https://salsa.debian.org/med-team/gatk | |
graphmap2 | | |
https://salsa.debian.org/med-team/graphmap2 | |
- ivar | | | new
| |
+ ivar | | | new
| ivar |
kallisto | amd64,arm64,ppc64el | main | bullseye,sid
| kallisto | kallisto
kraken2 | amd64,arm64,ppc64el | main | bullseye,sid
| kraken2 | kraken
libhts-dev | amd64,arm64,ppc64el | main |
buster,bullseye,sid | htslib |
lumpy | | |
| |
- manta | | |
https://salsa.debian.org/med-team/manta | |
+ manta | | |
https://salsa.debian.org/med-team/manta | manta |
megahit | | | new
| |
metabat | | |
| |
minia | amd64,arm64,ppc64el | main |
buster,bullseye,sid | | minia
@@ -78,15 +78,15 @@ Last-Update: Sun, 24 May 2020 10:42:41 +0200
r-cran-shazam | all | main |
buster,bullseye,sid | r-shazam |
r-cran-tigger | all | main |
buster,bullseye,sid | r-tigger |
rna-star | amd64,arm64,ppc64el | main |
buster,bullseye,sid | star | star
- r-other-ascat | | | new
| |
+ r-other-ascat | | | new
| ascat |
salmon | amd64 | main |
buster,bullseye,sid | salmon | salmon
samtools | amd64,arm64,ppc64el | main |
buster,bullseye,sid | samtools |
samtools
snakemake | all | main |
buster,bullseye,sid | snakemake |
snakemake
- snpeff | | |
https://salsa.debian.org/med-team/snpeff | |
- snpsift | | |
https://salsa.debian.org/med-team/snpeff | |
+ snpeff | | |
https://salsa.debian.org/med-team/snpeff | snpeff |
+ snpsift | | |
https://salsa.debian.org/med-team/snpeff | snpeff |
spades | amd64 | main |
buster,bullseye,sid | spades | Spades
sra-toolkit | amd64 | main |
buster,bullseye,sid | sra-tools |
sra-tools
- strelka | | |
https://salsa.debian.org/med-team/strelka | |
+ strelka | | |
https://salsa.debian.org/med-team/strelka | strelka |
tiddit | | |
| |
trim-galore | all | main | bullseye,sid
| trim-galore |
unicycler | amd64 | main |
buster,bullseye,sid | unicycler |
unicycler
=====================================
tasks/covid-19
=====================================
@@ -465,7 +465,6 @@ Recommends: toil
Recommends: umis
-
Recommends: workrave
X-Mark: <end>https://lists.debian.org/debian-med/2020/03/msg00142.html
@@ -473,3 +472,5 @@ X-Mark:
<end>https://lists.debian.org/debian-med/2020/03/msg00142.html
Recommends: python3-torch
Recommends: nextflow
+
+Recommends: quicktree
View it on GitLab:
https://salsa.debian.org/blends-team/med/-/compare/7e7e3834768efd7b021a888f3418d1fcd3f45c0e...0c9c2827bc22125b04ec0bb4abce6d7b43c494a6
--
View it on GitLab:
https://salsa.debian.org/blends-team/med/-/compare/7e7e3834768efd7b021a888f3418d1fcd3f45c0e...0c9c2827bc22125b04ec0bb4abce6d7b43c494a6
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