academic/pyCRAC: Updated for version 1.5.0.

Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

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

6 files changed, 26 insertions, 104 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..9eb56fc043 100644
--- a/academic/pyCRAC/README
+++ b/academic/pyCRAC/README
@@ -8,8 +8,6 @@ and reports sense and anti-sense hits.
 Included is the pipeline used for the analysis of a group of CRAC data
 sets.
 
-An R-function used for kinetic CRAC analysis can be found in
-/usr/share/pyCRAC-$VERSION/kinetic_crac_pipeline
 
 References
 
@@ -26,10 +24,9 @@ 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
@@ -44,4 +41,3 @@ 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..6482133f42 100644
--- a/academic/pyCRAC/pyCRAC.SlackBuild
+++ b/academic/pyCRAC/pyCRAC.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for pyCRAC
 
-# Copyright 2017 Rob van Nues
+# Copyright 2017-2021 Rob van Nues
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -23,7 +23,7 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=pyCRAC
-VERSION=${VERSION:-1.4.6}
+VERSION=${VERSION:-1.5.0}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -36,9 +36,9 @@ PYTHON2=false
 PYTHON3=true
 
 
-PIPENAM=kinetic_crac_pipeline
-PIPEVER=${PIPEVER:-ffe91cc6bf7a}
-PIPETAG=sgrann
+PIPENAM=crac_pipelines
+PIPEVER=master
+#PIPETAG=sgrann
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
@@ -73,20 +73,21 @@ rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
 rm -rf $PRGNAM-$VERSION
-rm -rf $PIPETAG-$PIPENAM-$PIPEVER
+#rm -rf $PIPETAG-$PIPENAM-$PIPEVER
+rm -rf $PIPENAM-$PIPEVER
 
 tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
 cd $PRGNAM-$VERSION
 mkdir $PRGNAM/$PIPENAM
 
-if [[ -f $CWD/$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
+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
-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
@@ -108,14 +109,12 @@ fi
 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
diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info
index 8048dd69ec..0b293a216a 100644
--- a/academic/pyCRAC/pyCRAC.info
+++ b/academic/pyCRAC/pyCRAC.info
@@ -1,10 +1,10 @@
 PRGNAM="pyCRAC"
-VERSION="1.4.6"
+VERSION="1.5.0"
 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"
+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"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="python3 flexbar novocraft numpy3 pysam scipy3 pandas ruffus"
diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py
index 421d43bebe..f76cd3868d 100644
--- a/academic/pyCRAC/setup_slack.py
+++ b/academic/pyCRAC/setup_slack.py
@@ -1,9 +1,9 @@
 #!/usr/bin/python
 
 __author__      = "Sander Granneman"
-__copyright__   = "Copyright 2019"
-__version__     = "1.4.6"
-__credits__     = ["Sander Granneman","Hywell Dunn Davies"]
+__copyright__   = "Copyright 2020"
+__version__     = "1.5.0"
+__credits__     = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"]
 __maintainer__  = ["Sander Granneman","Rob van Nues via SlackBuilds.org"]
 __email__       = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"]
 __status__      = "Production"
@@ -55,9 +55,8 @@ 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',
+					'pyCRAC/crac_pipelines/CRAC_pipeline_PE.py',
+					'pyCRAC/crac_pipelines/CRAC_pipeline_SE.py',
 				],
 	classifiers=[   'Development Status :: 5 - Production/Stable',
 					'Environment :: Console',
@@ -92,6 +91,3 @@ setup(name='pyCRAC',
 					'tests/genes.list'])
 				]
 			  )
-
-
-