[Blends-commit] [Git][blends-team/med][master] Synced with...
Andreas Tille
gitlab at salsa.debian.org
Wed Jun 17 09:19:35 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
59918ead by Andreas Tille at 2020-06-17T10:19:10+02:00
Synced with https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716, update UDD
- - - - -
2 changed files:
- covid-19_doc/bio_covid-19_dependencies_query
- covid-19_doc/bio_covid-19_dependencies_result
Changes:
=====================================
covid-19_doc/bio_covid-19_dependencies_query
=====================================
@@ -77,34 +77,42 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'shovill'),
(DEFAULT,'smartseq2'),
(DEFAULT,'viralcon'),
+(DEFAULT,'rosa'),
(DEFAULT,'nf-core'),
(DEFAULT,'abacas'),
+(DEFAULT,'adamjava'),
(DEFAULT,'allelecount'),
(DEFAULT,'python3-anndata'),
(DEFAULT,'libargs-dev'),
(DEFAULT,'arvados'),
(DEFAULT,'r-other-ascat'),
(DEFAULT,'assembly-stats'),
-(DEFAULT,'libatomicbitvector-dev'),
+(DEFAULT,'atropos'),
(DEFAULT,'augustus'),
+(DEFAULT,'bamkit'),
(DEFAULT,'bandage'),
(DEFAULT,'libbbhash-dev'),
(DEFAULT,'bcftools'),
(DEFAULT,'bedtools'),
+(DEFAULT,'biobambam2'),
(DEFAULT,'python3-biopython'),
(DEFAULT,'ncbi-blast+'), -- == blast
(DEFAULT,'bowtie2'),
(DEFAULT,'busco'),
(DEFAULT,'bustools'),
+(DEFAULT,'busybee'),
(DEFAULT,'bwa'),
(DEFAULT,'cat-bat'),
(DEFAULT,'centrifuge'),
(DEFAULT,'changeo'),
(DEFAULT,'python3-cooler'),
(DEFAULT,'cutadapt'),
+(DEFAULT,'python3-cyvcf2'),
(DEFAULT,'diamond-aligner'),
(DEFAULT,'python3-deeptools'),
+(DEFAULT,'degreport'),
(DEFAULT,'drop-seq-tools'),
+(DEFAULT,'r-bioc-edger'),
(DEFAULT,'fastp'),
(DEFAULT,'fastqc'),
(DEFAULT,'filtlong'),
@@ -113,10 +121,14 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'flye'),
(DEFAULT,'freebayes'),
(DEFAULT,'gatk'),
+(DEFAULT,'gffread'),
+(DEFAULT,'python3-gffutils'),
+(DEFAULT,'gindex'),
(DEFAULT,'tigr-glimmer'),
+(DEFAULT,'grabix'),
(DEFAULT,'graphmap2'),
(DEFAULT,'bio-guppy'),
-(DEFAULT,'python3-h5py'),
+(DEFAULT,'hisat2'),
(DEFAULT,'r-bioc-htsfilter'),
(DEFAULT,'libhts-dev'),
(DEFAULT,'python3-htseq'),
@@ -127,9 +139,11 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'kraken2'),
(DEFAULT,'radiant'), -- == krona - Debian had to change the name
(DEFAULT,'lighter'),
+(DEFAULT,'lsd'),
(DEFAULT,'lumpy-sv'),
(DEFAULT,'magicblast'),
(DEFAULT,'manta'),
+(DEFAULT,'marginalign'),
(DEFAULT,'mash'),
(DEFAULT,'masurca'),
(DEFAULT,'mcaller'),
@@ -150,20 +164,22 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'nanofilt'),
(DEFAULT,'nanolyse'),
(DEFAULT,'python3-nanomath'),
+(DEFAULT,'nanoplot'),
(DEFAULT,'nanopolish'),
(DEFAULT,'nanook'),
(DEFAULT,'nanoraw'),
(DEFAULT,'nanosv'),
+(DEFAULT,'python3-ncls'),
(DEFAULT,'ngmlr'),
(DEFAULT,'oncofuse'),
(DEFAULT,'optitype'),
-(DEFAULT,'nanoplot'),
+(DEFAULT,'pairtools'),
(DEFAULT,'parallel-fastq-dump'),
(DEFAULT,'python3-pauvre'),
+(DEFAULT,'picard-tools'),
(DEFAULT,'picopore'),
(DEFAULT,'pinfish'),
(DEFAULT,'plasmidid'),
-(DEFAULT,'picard-tools'),
(DEFAULT,'pilon'),
(DEFAULT,'pomoxis'),
(DEFAULT,'pore'),
@@ -203,6 +219,7 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'seqwish'),
(DEFAULT,'signalalign'),
(DEFAULT,'skesa'),
+(DEFAULT,'sniffles'),
(DEFAULT,'snpeff'),
(DEFAULT,'snpsift'),
(DEFAULT,'spades'),
@@ -231,6 +248,8 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'wham-align'),
(DEFAULT,'yanagiba'),
(DEFAULT,'yanosim'),
+(DEFAULT,'libatomicbitvector-dev'),
+(DEFAULT,'python3-h5py'),
(DEFAULT,'python3-numpy'),
(DEFAULT,'python3-pandas'),
(DEFAULT,'python3-toolz'),
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Wed, 17 Jun 2020 09:43:18 +0200
+Last-Update: Wed, 17 Jun 2020 10:15:01 +0200
package | architectures | section | releases | conda | bio.tools | testsuite
------------------------+---------------------+----------+-----------------------------------------------------+----------------------+---------------+-------------------------------------
@@ -12,34 +12,42 @@ Last-Update: Wed, 17 Jun 2020 09:43:18 +0200
shovill | | | | | |
smartseq2 | | | | | |
viralcon | | | | | |
+ rosa | | | | | |
nf-core | | | | | |
abacas | all | main | buster,bullseye,sid | | | autopkgtest
+ adamjava | | | | | |
allelecount | amd64,arm64,ppc64el | main | bullseye,sid | cancerit-allelecount | | autopkgtest-pkg-perl
python3-anndata | | | new | anndata | |
libargs-dev | | | new | | |
arvados | | | https://salsa.debian.org/med-team/arvados | | |
r-other-ascat | all | main | sid | ascat | | autopkgtest-pkg-r
assembly-stats | amd64,arm64,ppc64el | main | bullseye,sid | | | autopkgtest
- libatomicbitvector-dev | all | main | bullseye,sid | | | autopkgtest
+ atropos | amd64,arm64,ppc64el | main | bullseye,sid | atropos | atropos |
augustus | amd64,arm64,ppc64el | main | buster,bullseye,sid | augustus | AUGUSTUS | autopkgtest
+ bamkit | all | main | sid | | |
bandage | amd64,arm64,ppc64el | main | buster,bullseye,sid | bandage | bandage |
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
+ biobambam2 | amd64,arm64,ppc64el | main | sid | biobambam | biobambam | autopkgtest
python3-biopython | amd64,arm64,ppc64el | main | buster,bullseye,sid | | Biopython | autopkgtest
ncbi-blast+ | amd64,arm64,ppc64el | main | buster,bullseye,sid | blast | blast | autopkgtest
bowtie2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | bowtie2 | bowtie2 | autopkgtest
busco | all | main | bullseye,sid | busco | |
bustools | amd64,arm64,ppc64el | main | bullseye,sid | bustools | BUStools |
+ busybee | | | | | |
bwa | amd64,arm64,ppc64el | main | buster,bullseye,sid | bwa | BWA | autopkgtest
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 | | | https://salsa.debian.org/med-team/python-cooler | cooler | |
cutadapt | all | main | buster,bullseye,sid | cutadapt | cutadapt | autopkgtest-pkg-python
+ python3-cyvcf2 | amd64,arm64 | main | buster,bullseye,sid | cyvcf2 | | 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
+ degreport | | | | | |
drop-seq-tools | all | main | bullseye,sid | dropseq_tools | |
+ r-bioc-edger | amd64,arm64,ppc64el | main | bullseye,sid | bioconductor-edger | edger | autopkgtest, autopkgtest-pkg-r
fastp | amd64,arm64,ppc64el | main | buster,bullseye,sid | fastp | | autopkgtest
fastqc | all | main | buster,bullseye,sid | fastqc | FastQC | autopkgtest
filtlong | amd64,arm64,ppc64el | main | bullseye,sid | filtlong | | autopkgtest
@@ -48,10 +56,14 @@ Last-Update: Wed, 17 Jun 2020 09:43:18 +0200
flye | | | https://salsa.debian.org/med-team/flye | flye | |
freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid | freebayes | freebayes | autopkgtest
gatk | | | https://salsa.debian.org/med-team/gatk | gatk4 | |
+ gffread | amd64,arm64,ppc64el | main | bullseye,sid | gffread | gffread | autopkgtest
+ python3-gffutils | all | main | buster,bullseye,sid | gffutils | GFFutils | autopkgtest
+ gindex | | | | | |
tigr-glimmer | amd64,arm64,ppc64el | main | buster,bullseye,sid | glimmer | glimmer | autopkgtest
+ grabix | amd64,arm64,ppc64el | main | buster,bullseye,sid | grabix | | autopkgtest
graphmap2 | | | https://salsa.debian.org/med-team/graphmap2 | graphmap | |
bio-guppy | | | | | |
- python3-h5py | all | main | buster,bullseye,sid | | | autopkgtest
+ hisat2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | hisat2 | hisat2 | autopkgtest
r-bioc-htsfilter | all | main | bullseye,sid | | | autopkgtest, autopkgtest-pkg-r
libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid | htslib | | autopkgtest
python3-htseq | amd64,arm64,ppc64el | main | buster,bullseye,sid | htseq | htseq | autopkgtest
@@ -62,9 +74,11 @@ Last-Update: Wed, 17 Jun 2020 09:43:18 +0200
kraken2 | amd64,arm64,ppc64el | main | bullseye,sid | kraken2 | kraken | autopkgtest
radiant | all | main | buster,bullseye,sid | | krona |
lighter | | | new | lighter | |
+ lsd | | | | | |
lumpy-sv | | | new | lumpy-sv | |
magicblast | | | | | |
manta | | | https://salsa.debian.org/med-team/manta | manta | |
+ marginalign | | | | | |
mash | amd64,arm64,ppc64el | main | buster,bullseye,sid | mash | | autopkgtest
masurca | | | | | |
mcaller | | | | | |
@@ -85,20 +99,22 @@ Last-Update: Wed, 17 Jun 2020 09:43:18 +0200
nanofilt | | | | | |
nanolyse | | | https://salsa.debian.org/med-team/nanolyse | nanolyse | |
python3-nanomath | all | main | bullseye,sid | | | autopkgtest
+ nanoplot | | | https://salsa.debian.org/med-team/nanoplot | nanoplot | |
nanopolish | amd64,arm64 | main | buster,bullseye,sid | nanopolish | nanopolish | autopkgtest
nanook | all | main | buster,bullseye,sid | | NanoOK |
nanoraw | | | | | |
nanosv | | | new | nanosv | |
+ python3-ncls | | | new | | |
ngmlr | | | | | |
oncofuse | | | https://salsa.debian.org/med-team/oncofuse | | |
optitype | | | https://salsa.debian.org/med-team/optitype | | |
- nanoplot | | | https://salsa.debian.org/med-team/nanoplot | nanoplot | |
+ pairtools | | | | | |
parallel-fastq-dump | all | main | sid | parallel-fastq-dump | |
python3-pauvre | all | main | bullseye,sid | | | autopkgtest
+ picard-tools | amd64 | main | buster,bullseye,sid | picard | Picard_tools | autopkgtest
picopore | | | new | picopore | |
pinfish | | | | | |
plasmidid | | | https://salsa.debian.org/med-team/plasmidid | plasmidid | |
- picard-tools | amd64 | main | buster,bullseye,sid | picard | Picard_tools | autopkgtest
pilon | all | main | buster,bullseye,sid | pilon | pilon |
pomoxis | | | | | |
pore | | | | | |
@@ -138,6 +154,7 @@ Last-Update: Wed, 17 Jun 2020 09:43:18 +0200
seqwish | | | https://salsa.debian.org/med-team/seqwish | seqwish | |
signalalign | | | | | |
skesa | amd64 | main | bullseye,sid | skesa | |
+ sniffles | amd64,arm64,ppc64el | main | buster,bullseye,sid | sniffles | sniffles | autopkgtest
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 | autopkgtest
@@ -166,10 +183,12 @@ Last-Update: Wed, 17 Jun 2020 09:43:18 +0200
wham-align | amd64 | main | bullseye,sid | wham | wham |
yanagiba | | | | | |
yanosim | | | | | |
+ libatomicbitvector-dev | all | main | bullseye,sid | | | autopkgtest
+ python3-h5py | all | main | buster,bullseye,sid | | | autopkgtest
python3-numpy | amd64,arm64,ppc64el | main | buster,bullseye,sid | | | autopkgtest
python3-numpy | amd64,arm64,ppc64el | main | buster,bullseye,sid | | | autopkgtest
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
-(169 Zeilen)
+(188 Zeilen)
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/59918ead544a88748f0494659ab8e72c915df10b
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/59918ead544a88748f0494659ab8e72c915df10b
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