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commit a4e9bffad79431b49ba2d1a04c2decdc93bb4276 Author: Sascha Steinbiss <sa...@debian.org> Date: Mon Jan 29 14:44:05 2018 +0100 remove obsolete patch files --- debian/changelog | 9 +- debian/patches/add-shebang-line-to-getMummerStats | 11 -- debian/patches/adjust_required_pysam_version.patch | 17 --- debian/patches/remove-pypi-deps-from-setup-py | 17 --- debian/patches/samtools_fix.patch | 120 --------------------- debian/patches/spelling.patch | 13 --- 6 files changed, 7 insertions(+), 180 deletions(-) diff --git a/debian/changelog b/debian/changelog index 9c149c3..423d0b7 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,13 @@ -iva (1.0.8+ds-2) UNRELEASED; urgency=medium +iva (1.0.9+ds-1) unstable; urgency=medium + [ Steffen Moeller ] * debian/upstream/metadata: Added refs to registries - -- Steffen Moeller <moel...@debian.org> Thu, 03 Aug 2017 14:33:14 +0200 + [ Sascha Steinbiss ] + * New upstream release. + * Remove obsolete patch files. + + -- Sascha Steinbiss <sa...@debian.org> Fri, 26 Jan 2018 11:44:17 +0100 iva (1.0.8+ds-1) unstable; urgency=medium diff --git a/debian/patches/add-shebang-line-to-getMummerStats b/debian/patches/add-shebang-line-to-getMummerStats deleted file mode 100644 index d2f226c..0000000 --- a/debian/patches/add-shebang-line-to-getMummerStats +++ /dev/null @@ -1,11 +0,0 @@ -Description: Add shebang line to getMummerStats -Author: Jorge Soares <j.s.soa...@gmail.com> -Last-Update: 2014-12-08 ---- a/iva/gage/getMummerStats.sh -+++ b/iva/gage/getMummerStats.sh -@@ -1,3 +1,5 @@ -+#!/bin/sh -+ - FILENAME=$1 - SCRIPT_PATH=$2 - JAVA_PATH=$2:. diff --git a/debian/patches/adjust_required_pysam_version.patch b/debian/patches/adjust_required_pysam_version.patch deleted file mode 100644 index d93fe85..0000000 --- a/debian/patches/adjust_required_pysam_version.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: relax pysam version - Upstream has fixed pysm to version 0.8.3 because there are building issues - with newer versions and pip. These are not present in Debian, so I'm relaxing the - version requirements. -Author: Sascha Steinbiss <sas...@steinbiss.name> -Forwarded: not-needed, upstream insists on using 0.8.3 ---- a/setup.py -+++ b/setup.py -@@ -60,7 +60,7 @@ - install_requires=[ - 'pyfastaq >= 3.10.0', - 'networkx >= 1.7', -- 'pysam >= 0.8.1, <= 0.8.3', -+ 'pysam >= 0.8.1', - ], - license='GPLv3', - classifiers=[ diff --git a/debian/patches/remove-pypi-deps-from-setup-py b/debian/patches/remove-pypi-deps-from-setup-py deleted file mode 100644 index 946a8bf..0000000 --- a/debian/patches/remove-pypi-deps-from-setup-py +++ /dev/null @@ -1,17 +0,0 @@ -Description: Removes deps from setup.py -Author: Jorge Soares <j.s.soa...@gmail.com> -Last-Update: 2014-12-08 ---- a/setup.py -+++ b/setup.py -@@ -42,11 +42,6 @@ - scripts=glob.glob('scripts/*'), - test_suite='nose.collector', - tests_require=['nose >= 1.3'], -- install_requires=[ -- 'pyfastaq >= 3.10.0', -- 'networkx >= 1.7', -- 'pysam >= 0.8.1, <= 0.8.3', -- ], - license='GPLv3', - classifiers=[ - 'Development Status :: 4 - Beta', diff --git a/debian/patches/samtools_fix.patch b/debian/patches/samtools_fix.patch deleted file mode 100644 index 19233a9..0000000 --- a/debian/patches/samtools_fix.patch +++ /dev/null @@ -1,120 +0,0 @@ -From ed16c9b1a940fe11b14c8adfbe3853e889604ac4 Mon Sep 17 00:00:00 2001 -From: Sascha Steinbiss <sas...@steinbiss.name> -Date: Tue, 3 May 2016 18:48:07 +0100 -Subject: [PATCH 1/3] make IVA compatible with new 'samtools sort' syntax - ---- - iva/external_progs.py | 4 ++-- - iva/mapping.py | 6 +++++- - 2 files changed, 7 insertions(+), 3 deletions(-) - -diff --git a/iva/external_progs.py b/iva/external_progs.py -index 8b42054..c8056b1 100644 ---- a/iva/external_progs.py -+++ b/iva/external_progs.py -@@ -23,10 +23,10 @@ def is_in_path(prog): - 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), - 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), - 'smalt': ('smalt version', re.compile('^Version: (.*)$')), -- 'samtools': ('samtools', re.compile('^Version: (.*)$')), -+ 'samtools': ('samtools', re.compile('^Version: ([^ ]+)')), - } - -- -+ - minimum_versions = { - 'samtools': '0.1.19' - } -diff --git a/iva/mapping.py b/iva/mapping.py -index 681b5be..63bfd90 100644 ---- a/iva/mapping.py -+++ b/iva/mapping.py -@@ -5,6 +5,7 @@ - import pyfastaq - import pysam - from iva import common -+from iva import external_progs - - class Error (Exception): pass - -@@ -78,7 +79,10 @@ def map_reads(reads_fwd, reads_rev, ref_fa, out_prefix, index_k=15, index_s=3, t - if sort: - threads = min(4, threads) - thread_mem = int(500 / threads) -- sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix -+ if str(external_progs.get_version('samtools')) >= '1.2': -+ sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M -o ' + final_bam + ' ' + intermediate_bam -+ else: -+ sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix - index_cmd = 'samtools index ' + final_bam - if verbose >= 2: - print(' map reads. sort: ', sort_cmd) - -From 5fac89d891fb0932b60f06d8225f44a3642c2035 Mon Sep 17 00:00:00 2001 -From: Sascha Steinbiss <sas...@steinbiss.name> -Date: Wed, 4 May 2016 08:52:50 +0000 -Subject: [PATCH 2/3] clean up test directories - ---- - iva/qc_external.py | 7 ++++--- - 1 file changed, 4 insertions(+), 3 deletions(-) - -diff --git a/iva/qc_external.py b/iva/qc_external.py -index b04bbb1..ae76718 100644 ---- a/iva/qc_external.py -+++ b/iva/qc_external.py -@@ -142,9 +142,10 @@ def run_ratt(embl_dir, assembly, outdir, config_file=None, transfer='Species', c - cwd = os.getcwd() - try: - os.mkdir(outdir) -- os.chdir(outdir) - except: -- raise Error('Error mkdir ' + outdir) -+ pass -+ os.chdir(outdir) -+ iva.common.syscall('rm -rf ./*') - - extractor = iva.egg_extract.Extractor(os.path.abspath(os.path.join(os.path.dirname(iva.__file__), os.pardir))) - ratt_code_indir = os.path.join('iva', 'ratt') -@@ -200,7 +201,7 @@ def run_ratt(embl_dir, assembly, outdir, config_file=None, transfer='Species', c - except: - pass - -- iva.common.syscall('rm query.* Reference.* nucmer.* out.*') -+ iva.common.syscall('rm -f query.* Reference.* nucmer.* out.*') - - os.chdir(cwd) - return stats - -From 3b25765ac1eeb4bab5246087ed3c2ef6c0648e36 Mon Sep 17 00:00:00 2001 -From: Sascha Steinbiss <sas...@steinbiss.name> -Date: Wed, 4 May 2016 09:00:36 +0000 -Subject: [PATCH 3/3] make outdir recreation more robust - ---- - iva/qc_external.py | 11 ++++++----- - 1 file changed, 6 insertions(+), 5 deletions(-) - -diff --git a/iva/qc_external.py b/iva/qc_external.py -index ae76718..bed1c58 100644 ---- a/iva/qc_external.py -+++ b/iva/qc_external.py -@@ -140,12 +140,13 @@ def run_ratt(embl_dir, assembly, outdir, config_file=None, transfer='Species', c - assembly = os.path.abspath(assembly) - - cwd = os.getcwd() -- try: -- os.mkdir(outdir) -- except: -- pass -+ if os.path.exists(outdir): -+ if os.path.isdir(outdir): -+ shutil.rmtree(outdir) -+ else: -+ os.unlink(outdir) -+ os.mkdir(outdir) - os.chdir(outdir) -- iva.common.syscall('rm -rf ./*') - - extractor = iva.egg_extract.Extractor(os.path.abspath(os.path.join(os.path.dirname(iva.__file__), os.pardir))) - ratt_code_indir = os.path.join('iva', 'ratt') diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch deleted file mode 100644 index 128dec1..0000000 --- a/debian/patches/spelling.patch +++ /dev/null @@ -1,13 +0,0 @@ -Description: spelling fixes -Author: Sascha Steinbiss <sa...@debian.org> ---- a/scripts/iva_qc_make_db -+++ b/scripts/iva_qc_make_db -@@ -23,7 +23,7 @@ - ) - - parser.add_argument('outdir', help='Name of output directory', metavar='Directory_name') --parser.add_argument('--add_to_ref', action=iva.common.abspathAction, help='Filename of Genbank IDs or GI numbers to be added to database. Format is: whitespace separated list of GI numbers on each line. One line defines one genome (e.g. flu is 8 segements, so put 8 GI numbers on one line for one flu reference)', metavar='Filename') -+parser.add_argument('--add_to_ref', action=iva.common.abspathAction, help='Filename of Genbank IDs or GI numbers to be added to database. Format is: whitespace separated list of GI numbers on each line. One line defines one genome (e.g. flu is 8 segments, so put 8 GI numbers on one line for one flu reference)', metavar='Filename') - parser.add_argument('--skip_viruses', action='store_true', help='Do not run kraken-build --download-library viruses when building the database. If this option used, then --add_to_ref must also be used') - parser.add_argument('--threads', type=int, help='Number of threads to use [%(default)s]', metavar='INT', default=1) - parser.add_argument('--minimizer_len', type=int, help='Number to pass to kraken-build minimizer_len option [%(default)s]', default=13, metavar='INT') -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/iva.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit