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-rw-r--r--academic/pyCRAC/MANIFEST_slack.txt69
-rw-r--r--academic/pyCRAC/README28
-rw-r--r--academic/pyCRAC/README.tests2
-rw-r--r--academic/pyCRAC/pyCRAC.SlackBuild57
-rw-r--r--academic/pyCRAC/pyCRAC.info12
-rw-r--r--academic/pyCRAC/setup_slack.py16
6 files changed, 34 insertions, 150 deletions
diff --git a/academic/pyCRAC/MANIFEST_slack.txt b/academic/pyCRAC/MANIFEST_slack.txt
deleted file mode 100644
index 95a4931773..0000000000
--- a/academic/pyCRAC/MANIFEST_slack.txt
+++ /dev/null
@@ -1,69 +0,0 @@
-setup.py
-MANIFEST.txt
-LICENCE.txt
-README.txt
-pyCRAC/tests/test.novo
-pyCRAC/tests/test.sh
-pyCRAC/tests/test_coordinates.txt
-pyCRAC/tests/test.gtf
-pyCRAC/tests/test_f.fastq
-pyCRAC/tests/test_f.fastq.gz
-pyCRAC/tests/test_f_dm.fastq
-pyCRAC/tests/test_r.fastq
-pyCRAC/tests/test_r.fastq.gz
-pyCRAC/tests/test_r_dm.fastq
-pyCRAC/tests/indexes.txt
-pyCRAC/tests/barcodes.txt
-pyCRAC/tests/genes.lis
-pyCRAC/Classes/NGSFormatWriters.py
-pyCRAC/Classes/NGSFormatReaders.py
-pyCRAC/Classes/PairedReads.py
-pyCRAC/Classes/Pileups.py
-pyCRAC/Classes/Aligner.py
-pyCRAC/Classes/Motifs.py
-pyCRAC/Classes/Barcodes.py
-pyCRAC/Classes/Coverage.py
-pyCRAC/Classes/Exceptions.py
-pyCRAC/Classes/FDR.py
-pyCRAC/Classes/Clustering
-pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
-pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa
-pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
-pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
-pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py
-pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py
-pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py
-pyCRAC/kinetic_crac_pipeline/TrimNucs.py
-pyCRAC/scripts/pybed2GTF.py
-pyCRAC/scripts/pyGTF2bed.py
-pyCRaC/scripts/pyGTF2bedGraph.py
-pyCRAC/scripts/pyGTF2sgr.py
-pyCRAC/scripts/pyNormalizeIntervalLengths.py
-pyCRAC/scripts/pyFastqDuplicateRemover.py
-pyCRAC/scripts/pyFastqJoiner.py
-pyCRAC/scripts/pyFastqSplitter.py
-pyCRAC/scripts/pyGetGeneNamesFromGTF.py
-pyCRAC/scripts/pySelectMotifsFromGTF.py
-pyCRAC/scripts/pyGetGTFSources.py
-pyCRAC/scripts/pyFilterGTF.py
-pyCRAC/scripts/pyFasta2tab.py
-pyCRAC/scripts/pyAlignment2Tab.py
-pyCRAC/scripts/pyExtractLinesFromGTF.py
-pyCRAC/scripts/pyCheckGTFfile.py
-pyCRAC/scripts/pyCalculateChromosomeLengths.py
-pyCRAC/pyClusterReads.py
-pyCRAC/pyCalculateFDRs.py
-pyCRAC/pyCalculateMutationFrequencies.py
-pyCRAC/pyBinCollector.py
-pyCRAC/pyMotif.py
-pyCRAC/pyPileup.py
-pyCRAC/pyReadAligner.py
-pyCRAC/pyReadCounters.py
-pyCRAC/pyBarcodeFilter.py
-pyCRAC/Parsers/Blast.py
-pyCRAC/Parsers/GTF2.py
-pyCRAC/Parsers/Novoalign.py
-pyCRAC/Parsers/ParseAlignments.py
-pyCRAC/Parsers/SAM.py
-pyCRAC/Parsers/fasta2dict.py
-pyCRAC/Parsers/tab2dict.py
diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README
index 1583f3e62c..b9b74fd37b 100644
--- a/academic/pyCRAC/README
+++ b/academic/pyCRAC/README
@@ -5,11 +5,11 @@ 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.
+
-An R-function used for kinetic CRAC analysis can be found in
-/usr/share/pyCRAC-$VERSION/kinetic_crac_pipeline
References
@@ -25,23 +25,3 @@ A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G,
Granneman S.
If you want to run the test suite after installation, see README.tests.
-
-Note on the Crac pipelines:
-
-The CRAC_pipeline_PE.py and CRAC_pipeline_SE.py scripts now ONLY work
-with pyCRAC version 1.3.3 and Flexbar version 3.4.0 and later(!)
-Use the -h flag to get a detailed help menu.
-
-The CRAC_pipeline_PE.py script needs to be run from the folder that
-contains the fastq files
-
-The barcode list file should contain two tab-separated columns in which
-the first column is the barcode sequence and the second column is the
-name of the experiment
-
-The file containing the adapter sequences should be in the fasta format.
-
-The chromosome_lengths file should contain two tab-separated columns in
-which the first column has the chromosome name and the second the
-chromosome length.
-
diff --git a/academic/pyCRAC/README.tests b/academic/pyCRAC/README.tests
index ee98d3fdaa..e1b634e6a3 100644
--- a/academic/pyCRAC/README.tests
+++ b/academic/pyCRAC/README.tests
@@ -1,7 +1,7 @@
To test the pyCRAC scripts after installing the package on Slackware:
cp -R /usr/share/pyCRAC-$VERSION <path-to-your-work-directory>/
- cd <path-to-your-work-directory>/pyCRAC/tests
+ cd <path-to-your-work-directory>/pyCRAC-$VERSION/tests
sh test.sh
If all tests complete without an error, the package is working.
diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild
index f94cec426b..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 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=${VERSION:-1.4.6}
+VERSION=${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=kinetic_crac_pipeline
-PIPEVER=${PIPEVER:-ffe91cc6bf7a}
-PIPETAG=sgrann
+PKGTYPE=${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}
@@ -73,20 +70,12 @@ rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $PRGNAM-$VERSION
-rm -rf $PIPETAG-$PIPENAM-$PIPEVER
tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
cd $PRGNAM-$VERSION
-mkdir $PRGNAM/$PIPENAM
-
-if [[ -f $CWD/$PIPETAG-$PIPENAM-$PIPEVER.tar.gz ]]; then
- tar xvf $CWD/$PIPETAG-$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1
-elif [[ -f $CWD/$PIPEVER.tar.gz ]]; then
- tar xvf $CWD/$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1
-fi
#replace setup.py; test.sh
-rm setup.py
+mv setup.py setup.py.ORIG
cp $CWD/setup_slack.py setup.py
rm tests/test.sh
cp $CWD/test_slack.sh tests/test.sh
@@ -98,32 +87,24 @@ 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
-# The pipeline-R script
-mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM
-cp $PRGNAM/$PIPENAM/gaussianProcessAnalysis.R $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM
-
# the manual etc.
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
README.md \
+ setup.py.ORIG \
+ The_pyCRAC_Manual.pdf \
$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 8048dd69ec..8fcdeffd60 100644
--- a/academic/pyCRAC/pyCRAC.info
+++ b/academic/pyCRAC/pyCRAC.info
@@ -1,12 +1,10 @@
PRGNAM="pyCRAC"
-VERSION="1.4.6"
-HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/pycrac-software"
-DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.4.6.tar.gz \
- https://bitbucket.org/sgrann/kinetic_crac_pipeline/get/ffe91cc6bf7a.tar.gz"
-MD5SUM="ddbfbd08a5d8a178082056ef3efc99a8 \
- 8c19a15c439941cc5ae17e083f52143a"
+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 421d43bebe..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 2019"
-__version__ = "1.4.6"
-__credits__ = ["Sander Granneman","Hywell Dunn Davies"]
-__maintainer__ = ["Sander Granneman","Rob van Nues via SlackBuilds.org"]
+__copyright__ = "Copyright 2021"
+__version__ = "1.5.2"
+__credits__ = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"]
+__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=[
@@ -55,9 +55,6 @@ setup(name='pyCRAC',
'pyCRAC/scripts/pyGTF2bedGraph.py',
'pyCRAC/scripts/pyFilterGTF.py',
'pyCRAC/scripts/pyNormalizeIntervalLengths.py',
- 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py',
- 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py',
- 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py',
],
classifiers=[ 'Development Status :: 5 - Production/Stable',
'Environment :: Console',
@@ -92,6 +89,3 @@ setup(name='pyCRAC',
'tests/genes.list'])
]
)
-
-
-
generated by cgit v1.2.3 (git 2.26.2) at 2024-05-18 20:41:29 +0000