academic/pyCRAC: Updated for version 1.2.4.0.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

5 files changed, 11 insertions, 92 deletions

diff --git a/academic/pyCRAC/GTF2-scripts.patch b/academic/pyCRAC/GTF2-scripts.patch
deleted file mode 100644
index 35f9512876..0000000000
--- a/academic/pyCRAC/GTF2-scripts.patch
+++ /dev/null
@@ -1,79 +0,0 @@
-diff -Naur sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2bedGraph.py sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2bedGraph.py
---- sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2bedGraph.py	2017-09-11 15:11:12.000000000 +0100
-+++ sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2bedGraph.py	2017-09-10 00:47:13.014633000 +0100
-@@ -2,7 +2,7 @@
- # not compatible with python 3
- __author__		= "Sander Granneman"
- __copyright__	= "Copyright 2017"
--__version__		= "0.0.7"
-+__version__		= "0.0.6"
- __credits__		= ["Sander Granneman"]
- __maintainer__	= "Sander Granneman"
- __email__		= "sgrannem@staffmail.ed.ac.uk"
-@@ -80,14 +80,12 @@
- 	chromdata = processChromFile(chromlengthfile)
- 	###
- 	
--	normvalue = 1.0
--	if permillion and normvalue == 1.0:
--		assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
--		normvalue = float(data.mapped_reads)/1000000.0
--			
- 	while True:
- 		lines = data.readLineByLine()
--							# to normalize the data to per million reads
-+		normvalue = 1.0
-+		if permillion and normvalue == 1.0:
-+			assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
-+			normvalue = float(data.mapped_reads)/1000000.0								# to normalize the data to per million reads
- 		if current_chromosome and data.chromosome != current_chromosome or not lines:
- 			for strand in chromdict:
- 				start = 0
-diff -Naur sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2sgr.py sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2sgr.py
---- sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2sgr.py	2017-09-11 15:11:12.000000000 +0100
-+++ sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2sgr.py	2017-09-10 00:47:13.014633000 +0100
-@@ -1,8 +1,8 @@
- #!/usr/bin/python
- # not compatible with python 3
- __author__		= "Sander Granneman"
--__copyright__	= "Copyright 2017"
--__version__		= "0.0.6"
-+__copyright__	= "Copyright 2015"
-+__version__		= "0.0.5"
- __credits__		= ["Sander Granneman"]
- __maintainer__	= "Sander Granneman"
- __email__		= "sgrannem@staffmail.ed.ac.uk"
-@@ -13,7 +13,7 @@
- #	pyGTF2sgr.py
- #
- #
--#	Copyright (c) Sander Granneman 2017
-+#	Copyright (c) Sander Granneman 2015
- #	
- #	Permission is hereby granted, free of charge, to any person obtaining a copy
- #	of this software and associated documentation files (the "Software"), to deal
-@@ -73,12 +73,11 @@
- 	###
- 	
- 	normvalue = 1.0
--	if permillion:
--		assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
--		normvalue = float(data.mapped_reads)/1000000.0
--
- 	while True:
- 		lines = data.readLineByLine()
-+		if permillion and normvalue == 1.0:
-+			assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
-+			normvalue = float(data.mapped_reads)/1000000.0
- 		if current_chromosome and data.chromosome != current_chromosome or not lines:
- 			for strand in strands:
- 				if min_cov:
-@@ -118,6 +117,8 @@
- 			if data.substitutions: chromdict[data.strand][data.substitutions] += data.number_of_reads
- 		elif type == "deletions":
- 			if data.deletions: chromdict[data.strand][data.deletions] += data.number_of_reads
-+		else:
-+			break
- 			
- def gtf2dropoffrates(gtffile,chromosomedata,out_files=[],score=False,log=sys.stdout,zeros=False,min_cov=0):
- 	"""Produces an sgr output file for hits, substitutions and deletions. It requires, besides data a file containing 
diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README
index dd847d0935..a5be782d73 100644
--- a/academic/pyCRAC/README
+++ b/academic/pyCRAC/README
@@ -1,8 +1,8 @@
 The pyCRAC package is a collection of python2-scripts to analyse high
-throughput data generated by RNA-sequencing, especially of molecules 
-crosslinked by UV to an immunoprecipitated protein of interest (i.e. 
-data generated by CLIP or CRAC protocols). 
-It can be used to remove duplicate reads,tackles directional libraries 
+throughput data generated by RNA-sequencing, especially of molecules
+crosslinked by UV to an immunoprecipitated protein of interest (i.e.
+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
diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild
index 7a386f452d..89f9a3fd65 100644
--- a/academic/pyCRAC/pyCRAC.SlackBuild
+++ b/academic/pyCRAC/pyCRAC.SlackBuild
@@ -23,12 +23,12 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=pyCRAC
-VERSION=${VERSION:-1.2.3.0}
+VERSION=${VERSION:-1.2.4.0}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 SRCNAM=sgrann-pycrac
-SRCVER=${SRCVER:-8792459eeef7}
+SRCVER=${SRCVER:-eadda2b95c34}
 
 PIPENAM=kinetic_crac_pipeline
 PIPEVER=${PIPEVER:-73dff1be9488}
@@ -73,8 +73,6 @@ mkdir $PRGNAM/$PIPENAM
 tar xvf $CWD/sgrann-$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 || \
   tar xvf $CWD/$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1
 
-patch -p1 < $CWD/GTF2-scripts.patch
-
 #replace setup.py
 rm setup.py
 cp $CWD/setup_slack.py setup.py
@@ -94,7 +92,7 @@ python setup.py install --root=$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 
+# The pipeline-R script
 mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM
 cp $PRGNAM/$PIPENAM/gaussianProcessAnalysis.R $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM
 
diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info
index 9051b43654..30f4980f21 100644
--- a/academic/pyCRAC/pyCRAC.info
+++ b/academic/pyCRAC/pyCRAC.info
@@ -1,9 +1,9 @@
 PRGNAM="pyCRAC"
-VERSION="1.2.3.0"
+VERSION="1.2.4.0"
 HOMEPAGE="https://bitbucket.org/sgrann/"
-DOWNLOAD="https://bitbucket.org/sgrann/pycrac/get/8792459eeef7.tar.gz \
+DOWNLOAD="https://bitbucket.org/sgrann/pycrac/get/eadda2b95c34.tar.gz \
           https://bitbucket.org/sgrann/kinetic_crac_pipeline/get/73dff1be9488.tar.gz"
-MD5SUM="a0e05b812dc765a2b1f673078ea43e3d \
+MD5SUM="c6b37913a6f7da123e3243166806aa56 \
         8f968d1dca38aa2b3ac401ba8da70cef"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py
index 621b944573..334e9c6a82 100644
--- a/academic/pyCRAC/setup_slack.py
+++ b/academic/pyCRAC/setup_slack.py
@@ -2,7 +2,7 @@
 # not compatible with python 3
 __author__      = "Sander Granneman"
 __copyright__   = "Copyright 2017"
-__version__     = "1.2.3.0"
+__version__     = "1.2.4.0"
 __credits__     = ["Sander Granneman","Hywell Dunn Davies"]
 __maintainer__  = ["Rob van Nues, via SlackBuilds.org"]
 __email__       = "sgrannem@staffmail.ed.ac.uk"