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academic/pyCRAC: Updated to version 1.5.2; crac_pipeline no longer included (see README)
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
brobr
Willy Sudiarto Raharjo
parent
b6e89350bb
commit
99d572de54
4 changed files with 13 additions and 47 deletions
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@ -5,8 +5,10 @@ data generated by CLIP or CRAC protocols).
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It can be used to remove duplicate reads,tackles directional libraries
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and reports sense and anti-sense hits.
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Included is the pipeline used for the analysis of a group of CRAC data
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sets.
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A pipeline that streamlines the analysis of a group of CRAC datasets
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is available at https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines and
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depends on the python package 'ruffus', also at slackbuilds.org.
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References
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@ -23,21 +25,3 @@ A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G,
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Granneman S.
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If you want to run the test suite after installation, see README.tests.
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Note on the Crac pipelines:
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Use the -h flag to get a detailed help menu.
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The CRAC_pipeline_PE.py script needs to be run from the folder that
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contains the fastq files
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The barcode list file should contain two tab-separated columns in which
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the first column is the barcode sequence and the second column is the
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name of the experiment
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The file containing the adapter sequences should be in the fasta format.
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The chromosome_lengths file should contain two tab-separated columns in
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which the first column has the chromosome name and the second the
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chromosome length.
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@ -2,7 +2,7 @@
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# Slackware build script for pyCRAC
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# Copyright 2017-2021 Rob van Nues
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# Copyright 2017-2023 Rob van Nues
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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@ -25,15 +25,11 @@
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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=pyCRAC
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VERSION=${VERSION:-1.5.1}
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VERSION=${VERSION:-1.5.2}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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PIPENAM=crac_pipelines
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PIPEVER=b2647bae8c515fa3a790db3459342adb826a0a6a
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#PIPETAG=sgrann
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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@ -74,18 +70,9 @@ rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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#rm -rf $PIPETAG-$PIPENAM-$PIPEVER
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rm -rf $PIPENAM-$PIPEVER
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tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
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cd $PRGNAM-$VERSION
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mkdir $PRGNAM/$PIPENAM
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if [[ -f $CWD/$PIPENAM-$PIPEVER.tar.gz ]]; then
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tar xvf $CWD/$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1
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else
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echo "$PIPENAM-$PIPEVER.tar.gz not found"
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fi
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#replace setup.py; test.sh
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mv setup.py setup.py.ORIG
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@ -114,7 +101,6 @@ cp -a \
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$CWD/README.tests $CWD/setup_slack.py \
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$CWD/README \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cp -a $PRGNAM/$PIPENAM/README.md $PKG/usr/doc/$PRGNAM-$VERSION/$PIPENAM-README.md
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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@ -1,12 +1,10 @@
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PRGNAM="pyCRAC"
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VERSION="1.5.1"
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HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/pycrac-software"
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DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.1.tar.gz \
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https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines/-/archive/b2647bae8c515fa3a790db3459342adb826a0a6a/crac_pipelines-b2647bae8c515fa3a790db3459342adb826a0a6a.tar.gz"
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MD5SUM="f634167e03ef26213efb4400671dbc9c \
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dc396811a0df2c83cb52681c94e8cb69"
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VERSION="1.5.2"
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HOMEPAGE="https://git.ecdf.ed.ac.uk/sgrannem/pycrac"
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DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.2.tar.gz"
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MD5SUM="f2bbb5dbcbe2b17051b8843a7e4d519f"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="flexbar novocraft python3-numpy pysam python3-scipy pandas ruffus"
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REQUIRES="flexbar novocraft python3-numpy pysam python3-scipy python3-pandas"
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MAINTAINER="Rob van Nues"
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EMAIL="sborg63@disroot.org"
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@ -2,7 +2,7 @@
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__author__ = "Sander Granneman"
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__copyright__ = "Copyright 2021"
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__version__ = "1.5.1"
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__version__ = "1.5.2"
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__credits__ = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"]
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__maintainer__ = ["Sander Granneman","Rob van Nues for SlackBuilds.org"]
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__email__ = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"]
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@ -25,7 +25,7 @@ setup(name='pyCRAC',
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description='Python NextGen sequencing data processing software',
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author='Sander Granneman',
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author_email='sgrannem@staffmail.ed.ac.uk',
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url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html',
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url='https://git.ecdf.ed.ac.uk/sgrannem/pycrac',
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packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'],
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install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6','six >= 1.9.0'],
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scripts=[
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@ -55,8 +55,6 @@ setup(name='pyCRAC',
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'pyCRAC/scripts/pyGTF2bedGraph.py',
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'pyCRAC/scripts/pyFilterGTF.py',
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'pyCRAC/scripts/pyNormalizeIntervalLengths.py',
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'pyCRAC/crac_pipelines/CRAC_pipeline_PE.py',
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'pyCRAC/crac_pipelines/CRAC_pipeline_SE.py',
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],
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classifiers=[ 'Development Status :: 5 - Production/Stable',
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'Environment :: Console',
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