diff options
Diffstat (limited to 'academic/pyCRAC')
| -rw-r--r-- | academic/pyCRAC/README | 24 | ||||
| -rw-r--r-- | academic/pyCRAC/pyCRAC.SlackBuild | 50 | ||||
| -rw-r--r-- | academic/pyCRAC/pyCRAC.info | 12 | ||||
| -rw-r--r-- | academic/pyCRAC/setup_slack.py | 10 |
4 files changed, 29 insertions, 67 deletions
diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README index 9eb56fc043..b9b74fd37b 100644 --- a/academic/pyCRAC/README +++ b/academic/pyCRAC/README @@ -5,8 +5,10 @@ data generated by CLIP or CRAC protocols). It can be used to remove duplicate reads,tackles directional libraries and reports sense and anti-sense hits. -Included is the pipeline used for the analysis of a group of CRAC data -sets. +A pipeline that streamlines the analysis of a group of CRAC datasets +is available at https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines and +depends on the python package 'ruffus', also at slackbuilds.org. + References @@ -23,21 +25,3 @@ A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G, Granneman S. If you want to run the test suite after installation, see README.tests. - - -Note on the Crac pipelines: - -Use the -h flag to get a detailed help menu. - -The CRAC_pipeline_PE.py script needs to be run from the folder that -contains the fastq files - -The barcode list file should contain two tab-separated columns in which -the first column is the barcode sequence and the second column is the -name of the experiment - -The file containing the adapter sequences should be in the fasta format. - -The chromosome_lengths file should contain two tab-separated columns in -which the first column has the chromosome name and the second the -chromosome length. diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild index 6482133f42..038db738b1 100644 --- a/academic/pyCRAC/pyCRAC.SlackBuild +++ b/academic/pyCRAC/pyCRAC.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pyCRAC -# Copyright 2017-2021 Rob van Nues +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,23 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pyCRAC -VERSION=${VERSION:-1.5.0} +VERSION=${VERSION:-1.5.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} - -# pyCRAC works with python2 as well as python3; -# Note that python2 is being phased out; therefore python3 is set as default. -# This is the same for the python pyCrac dependencies - -#set which python version to install it for -PYTHON2=false -PYTHON3=true - - -PIPENAM=crac_pipelines -PIPEVER=master -#PIPETAG=sgrann +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -48,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -73,18 +70,9 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -#rm -rf $PIPETAG-$PIPENAM-$PIPEVER -rm -rf $PIPENAM-$PIPEVER tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -mkdir $PRGNAM/$PIPENAM - -if [[ -f $CWD/$PIPENAM-$PIPEVER.tar.gz ]]; then - tar xvf $CWD/$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 -else - echo "$PIPENAM-$PIPEVER.tar.gz not found" -fi #replace setup.py; test.sh mv setup.py setup.py.ORIG @@ -99,12 +87,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -if $PYTHON2; then - python setup.py install --root=$PKG -fi -if $PYTHON3; then - python3 setup.py install --root=$PKG -fi +python3 setup.py install --root=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -118,11 +101,10 @@ cp -a \ $CWD/README.tests $CWD/setup_slack.py \ $CWD/README \ $PKG/usr/doc/$PRGNAM-$VERSION -cp -a $PRGNAM/$PIPENAM/README.md $PKG/usr/doc/$PRGNAM-$VERSION/$PIPENAM-README.md cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info index 0b293a216a..8fcdeffd60 100644 --- a/academic/pyCRAC/pyCRAC.info +++ b/academic/pyCRAC/pyCRAC.info @@ -1,12 +1,10 @@ PRGNAM="pyCRAC" -VERSION="1.5.0" -HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/pycrac-software" -DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.0.tar.gz \ - https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines/-/archive/master/crac_pipelines-master.tar.gz" -MD5SUM="73bfb92e8ae0f30fd73f21a77d265288 \ - 119c67d318a03ed29471e4caeb2690a4" +VERSION="1.5.2" +HOMEPAGE="https://git.ecdf.ed.ac.uk/sgrannem/pycrac" +DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.2.tar.gz" +MD5SUM="f2bbb5dbcbe2b17051b8843a7e4d519f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="python3 flexbar novocraft numpy3 pysam scipy3 pandas ruffus" +REQUIRES="flexbar novocraft pysam python3-scipy python3-pandas" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py index f76cd3868d..db5c30751f 100644 --- a/academic/pyCRAC/setup_slack.py +++ b/academic/pyCRAC/setup_slack.py @@ -1,10 +1,10 @@ #!/usr/bin/python __author__ = "Sander Granneman" -__copyright__ = "Copyright 2020" -__version__ = "1.5.0" +__copyright__ = "Copyright 2021" +__version__ = "1.5.2" __credits__ = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"] -__maintainer__ = ["Sander Granneman","Rob van Nues via SlackBuilds.org"] +__maintainer__ = ["Sander Granneman","Rob van Nues for SlackBuilds.org"] __email__ = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"] __status__ = "Production" @@ -25,7 +25,7 @@ setup(name='pyCRAC', description='Python NextGen sequencing data processing software', author='Sander Granneman', author_email='sgrannem@staffmail.ed.ac.uk', - url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html', + url='https://git.ecdf.ed.ac.uk/sgrannem/pycrac', packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'], install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6','six >= 1.9.0'], scripts=[ @@ -55,8 +55,6 @@ setup(name='pyCRAC', 'pyCRAC/scripts/pyGTF2bedGraph.py', 'pyCRAC/scripts/pyFilterGTF.py', 'pyCRAC/scripts/pyNormalizeIntervalLengths.py', - 'pyCRAC/crac_pipelines/CRAC_pipeline_PE.py', - 'pyCRAC/crac_pipelines/CRAC_pipeline_SE.py', ], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Environment :: Console', |