[med-svn] [Git][med-team/bcbio][master] Series of updates.
Steffen Möller
gitlab at salsa.debian.org
Sat Nov 14 18:24:45 GMT 2020
Steffen Möller pushed to branch master at Debian Med / bcbio
Commits:
e23c8f36 by Steffen Moeller at 2020-11-14T19:24:21+01:00
Series of updates.
- - - - -
7 changed files:
- debian/TODO
- debian/control
- + debian/patches/collectionsAbc.patch
- + debian/patches/hts_nim_tools.patch
- + debian/patches/pytest2to3.patch
- + debian/patches/pythonpaths.patch
- debian/patches/series
Changes:
=====================================
debian/TODO
=====================================
@@ -45,7 +45,6 @@ convinced that this is no longer required.
#py # conda-specific
python-dateutil >=2.5.0 # likely obsolete?
pyyaml https://pyyaml.org/wiki/PyYAML
- python3-seqcluster # to be reuploaded
To be packaged
fadapa https://github.com/fadapa/fadapa
pycrypto
@@ -82,7 +81,7 @@ convinced that this is no longer required.
pyvcf
requests
scipy >=1.3.0
- seqcluster
+ seqcluster (python3-seqcluster)
statsmodels
tabulate
toolz
@@ -119,27 +118,14 @@ package python-seqcluster (to be reuploaded)
Packages presumed easy to package
---------------------------------
-
-package hts_nim_tools
- https://github.com/brentp/hts-nim-tools
- Likely addressed with the other efforts on nim behind mosdepth
- salsa
-
package "asl solver"
http://www.ampl.com/netlib/ampl/solvers.tgz
needed by gjh_asl_json
-
-r-bioc-HTSFilter
https://bioconductor.org/packages/release/bioc/html/HTSFilter.html
Needed by seqcluster
needs r-bioc-edger and r-bioc-deseq (also deseq2) as build dependends which are not in Debian
-r-bioc-DEGreport
- https://bioconductor.org/packages/release/bioc/html/DEGreport.html
- Needed by seqcluster
- needs r-bioc-edger and other dependencies which are not in Debian
-
Packages of importance for basic NGS workflows with motivation beyond bcbio
---------------------------------------------------------------------------
@@ -152,13 +138,6 @@ package optitype
https://salsa.debian.org/med-team/optitype (rudimentary)
Stuck over too many dependencies
-package vcfanno
- https://salsa.debian.org/med-team/vcfanno
- Not fun because of many GO packages that are still missing,
- "biogo" being one of them.
- Stuck over too many dependencies
-
-
Difficult to package to the degree that one is tempted to use conda for the meantime
------------------------------------------------------------------------------------
@@ -195,13 +174,6 @@ package sailfish
https://salsa.debian.org/med-team/sailfish
FTBFS
-package vt
- https://github.com/atks/vt
-
-package Rmath
- https://github.com/atks/Rmath
- needed by vt
-
package fgbio
https://github.com/fulcrumgenomics/fgbio
Anyone much into scala?
=====================================
debian/control
=====================================
@@ -22,15 +22,23 @@ Build-Depends: debhelper-compat (= 13),
python3-joblib,
# for testing
atropos <!nocheck>,
+ bcftools <!nocheck>,
bedtools <!nocheck>,
biobambam2 <!nocheck>,
+ bowtie2 <!nocheck>,
+ cnvkit <!nocheck>,
+ fastqc <!nocheck>,
+ freebayes <!nocheck>,
gffread <!nocheck>,
grabix <!nocheck>,
hisat2 <!nocheck>,
+ hts-nim-tools <!nocheck>,
mosdepth <!nocheck>,
multiqc <!nocheck>,
perl <!nocheck>,
libpicard-java <!nocheck>,
+ libvcflib-tools <!nocheck>,
+ picard-tools <!nocheck>,
python3-biopython <!nocheck>,
python3-cyvcf2 <!nocheck>,
python3-geneimpacts <!nocheck>,
@@ -39,14 +47,26 @@ Build-Depends: debhelper-compat (= 13),
python3-requests <!nocheck>,
python3-pytest <!nocheck>,
python3-pytest-mock <!nocheck>,
- bcftools <!nocheck>,
+ python3-seqcluster <!nocheck>,
+ pythonpy <!nocheck>,
+ rapmap <!nocheck>,
rna-star <!nocheck>,
+ r-other-wasabi <!nocheck>,
+ r-bioc-htsfilter <!nocheck>,
+ r-bioc-degreport <!nocheck>,
+ r-cran-tidyverse <!nocheck>,
+ r-bioc-tximport <!nocheck>,
salmon <!nocheck>,
samblaster <!nocheck>,
samtools <!nocheck>,
+ seqan-apps <!nocheck>,
seqtk <!nocheck>,
+ subread <!nocheck>,
tabix <!nocheck>,
tophat-recondition <!nocheck>,
+ umis <!nocheck>,
+ vcfanno <!nocheck>,
+ vt <!nocheck>,
wham-align <!nocheck>,
xonsh <!nocheck>,
# documentation
@@ -74,6 +94,7 @@ Depends: ${python3:Depends},
python3-six,
python3-tornado
Recommends:
+ cnvkit,
mosdepth,
multiqc,
python3-arrow,
@@ -83,6 +104,8 @@ Recommends:
python3-seqcluster,
python3-statsmodels,
python3-tabulate,
+ seqan-apps,
+ vcfanno,
vt
Suggests:
bcbio-doc,
=====================================
debian/patches/collectionsAbc.patch
=====================================
@@ -0,0 +1,14 @@
+Index: bcbio/bcbio/utils.py
+===================================================================
+--- bcbio.orig/bcbio/utils.py
++++ bcbio/bcbio/utils.py
+@@ -19,7 +19,8 @@ import six
+ import toolz as tz
+ import yaml
+
+-from collections import Mapping, OrderedDict
++from collections.abc import Mapping
++from collections import OrderedDict
+
+
+ try:
=====================================
debian/patches/hts_nim_tools.patch
=====================================
@@ -0,0 +1,28 @@
+Index: bcbio/bcbio/bam/readstats.py
+===================================================================
+--- bcbio.orig/bcbio/bam/readstats.py
++++ bcbio/bcbio/bam/readstats.py
+@@ -89,7 +89,7 @@ def number_of_mapped_reads(data, bam_fil
+ bam.index(bam_file, data["config"], check_timestamp=False)
+ num_cores = dd.get_num_cores(data)
+ with file_transaction(data, count_file) as tx_out_file:
+- cmd = ("hts_nim_tools count-reads -t {num_cores} -F {flag} {bed_file} {bam_file} > {tx_out_file}")
++ cmd = ("hts-nim-tools count-reads -t {num_cores} -F {flag} {bed_file} {bam_file} > {tx_out_file}")
+ do.run(cmd.format(**locals()), "Count mapped reads: %s" % (dd.get_sample_name(data)))
+ count = 0
+ with open(count_file) as in_handle:
+Index: bcbio/docs/contents/internals.md
+===================================================================
+--- bcbio.orig/docs/contents/internals.md
++++ bcbio/docs/contents/internals.md
+@@ -137,8 +137,8 @@ resources:
+ ```
+ 1. hts_nim counts:
+ ```shell
+- hts_nim_tools count-reads -t 16 -F 1804 /path/samplex/counts/fullgenome.bed samplex-sort-cumi.bam > fullgenome-1804-counts.txt
+- hts_nim_tools count-reads -t 16 -F 1804 cleaned-target.bed samplex-sort-cumi.bam > cleaned-target-merged-1804-counts.txt
++ hts-nim-tools count-reads -t 16 -F 1804 /path/samplex/counts/fullgenome.bed samplex-sort-cumi.bam > fullgenome-1804-counts.txt
++ hts-nim-tools count-reads -t 16 -F 1804 cleaned-target.bed samplex-sort-cumi.bam > cleaned-target-merged-1804-counts.txt
+ ```
+ 1. samtools read statistics::
+ ```shell
=====================================
debian/patches/pytest2to3.patch
=====================================
@@ -0,0 +1,10 @@
+Index: bcbio/tests/run_tests.sh
+===================================================================
+--- bcbio.orig/tests/run_tests.sh
++++ bcbio/tests/run_tests.sh
+@@ -30,4 +30,4 @@ export PYTHONNOUSERSITE=1
+ if [ -d "../bcbio/pipeline" ]; then
+ [ -f ../bcbio/pipeline/version.py ] || touch ../bcbio/pipeline/version.py
+ fi
+-"$BCBIO_DIR/py.test" -p no:cacheprovider -p no:stepwise -v -s -m ${MARK} "$@"
++py.test-3 -p no:cacheprovider -p no:stepwise -v -s -m ${MARK} "$@"
=====================================
debian/patches/pythonpaths.patch
=====================================
@@ -0,0 +1,74 @@
+Index: bcbio/scripts/bcbio_fastq_umi_prep.py
+===================================================================
+--- bcbio.orig/scripts/bcbio_fastq_umi_prep.py
++++ bcbio/scripts/bcbio_fastq_umi_prep.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """Convert fastq inputs into paired inputs with UMIs in read names.
+
+ Handles three cases:
+Index: bcbio/scripts/bcbio_nextgen_install.py
+===================================================================
+--- bcbio.orig/scripts/bcbio_nextgen_install.py
++++ bcbio/scripts/bcbio_nextgen_install.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """Automatically install required tools and data to run bcbio-nextgen pipelines.
+
+ This automates the steps required for installation and setup to make it easier to get started with
+Index: bcbio/scripts/bcbio_nextgen.py
+===================================================================
+--- bcbio.orig/scripts/bcbio_nextgen.py
++++ bcbio/scripts/bcbio_nextgen.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python -Es
++#!/usr/bin/python3 -s
+ """Run an automated analysis pipeline for high throughput sequencing data.
+
+ Handles runs in local or distributed mode based on the command line or
+Index: bcbio/scripts/bcbio_setup_genome.py
+===================================================================
+--- bcbio.orig/scripts/bcbio_setup_genome.py
++++ bcbio/scripts/bcbio_setup_genome.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python -Es
++#!/usr/bin/python3 -Es
+ """
+ Script to set up a custom genome for bcbio-nextgen
+ """
+Index: bcbio/scripts/cwl/arvados_bcbio_runtimes.py
+===================================================================
+--- bcbio.orig/scripts/cwl/arvados_bcbio_runtimes.py
++++ bcbio/scripts/cwl/arvados_bcbio_runtimes.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """Summarize runtimes for bcbio Arvados CWL runs.
+
+ Usage:
+Index: bcbio/scripts/cwltool2wdl.py
+===================================================================
+--- bcbio.orig/scripts/cwltool2wdl.py
++++ bcbio/scripts/cwltool2wdl.py
+@@ -1,4 +1,4 @@
+-#!/bin/env python
++#!/usr/bin/python3
+ """Exploratory code to convert bcbio generated CWL into WDL.
+
+ Uses cwltool parser to parse input CWL then, calls out to cwl2wdl
+Index: bcbio/tests/run_tests.sh
+===================================================================
+--- bcbio.orig/tests/run_tests.sh
++++ bcbio/tests/run_tests.sh
+@@ -24,7 +24,8 @@ else
+ fi
+
+ unset PYTHONHOME
+-unset PYTHONPATH
++export PATH=$(pwd)/scripts:$PATH
++export PYTHONPATH=$(pwd)
+ export PYTHONNOUSERSITE=1
+ # Ensure version.py exists in raw cloned bcbio directory
+ if [ -d "../bcbio/pipeline" ]; then
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,8 @@
#spelling
+pytest2to3.patch
include_tests
#add_installed_dir_paths.patch
do_not_use_git.patch
+pythonpaths.patch
+hts_nim_tools.patch
+collectionsAbc.patch
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49
--
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49
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