academic/pyCRAC: Updated to version 1.5.2; crac_pipeline no longer included (see README)

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

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.

academic/pyCRAC/pyCRAC.SlackBuild

@@ -2,7 +2,7 @@
 
 # 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
@@ -25,15 +25,11 @@
 cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=pyCRAC
-VERSION=${VERSION:-1.5.1}
+VERSION=${VERSION:-1.5.2}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
 
-PIPENAM=crac_pipelines
-PIPEVER=b2647bae8c515fa3a790db3459342adb826a0a6a
-#PIPETAG=sgrann
-
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
     i?86) ARCH=i586 ;;
@@ -74,18 +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
@@ -114,7 +101,6 @@ 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

academic/pyCRAC/pyCRAC.info

@@ -1,12 +1,10 @@
 PRGNAM="pyCRAC"
-VERSION="1.5.1"
-HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/pycrac-software"
-DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.1.tar.gz \
-          https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines/-/archive/b2647bae8c515fa3a790db3459342adb826a0a6a/crac_pipelines-b2647bae8c515fa3a790db3459342adb826a0a6a.tar.gz"
-MD5SUM="f634167e03ef26213efb4400671dbc9c \
-        dc396811a0df2c83cb52681c94e8cb69"
+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="flexbar novocraft python3-numpy pysam python3-scipy pandas ruffus"
+REQUIRES="flexbar novocraft python3-numpy pysam python3-scipy python3-pandas"
 MAINTAINER="Rob van Nues"
 EMAIL="sborg63@disroot.org"

academic/pyCRAC/setup_slack.py

@@ -2,7 +2,7 @@
 
 __author__      = "Sander Granneman"
 __copyright__   = "Copyright 2021"
-__version__     = "1.5.1"
+__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"]
@@ -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',