diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/pyCRAC/MANIFEST_slack.txt | 69 | ||||
| -rw-r--r-- | academic/pyCRAC/README | 6 | ||||
| -rw-r--r-- | academic/pyCRAC/README.tests | 2 | ||||
| -rw-r--r-- | academic/pyCRAC/pyCRAC.SlackBuild | 29 | ||||
| -rw-r--r-- | academic/pyCRAC/pyCRAC.info | 10 | ||||
| -rw-r--r-- | academic/pyCRAC/setup_slack.py | 14 |
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']) ] ) - - - |