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author Rob van Nues <sborg63@disroot.org>2019-07-16 11:12:59 -0500
committer Robby Workman <rworkman@slackbuilds.org>2019-07-19 22:33:45 -0500
commit321d78de8d11c25bb0fad9341eb2ac306c987ead (patch)
treec97425ad0dfb2196d645909a6862923be747951d
parent1b0aba303888b938f7679da7938027bc29ace85e (diff)
downloadslackbuilds-pyCRAC-nomerge.tar.gz
slackbuilds-pyCRAC-nomerge.tar.xz
academic/pyCRAC: Updated for version 1.4.5.pyCRAC-nomerge
This needs some work based on recent feedback from the maintainer: QUOTE Please use scipy3; although users could use python2 with this, the packages are set up for python3. Apart from scipy, also numpy needs to be set for python3: numpy3. Further, I noticed that the pandas.Slackbuild does not cater for python3 whereas it works fine in that environment. Could you, or Dimitris be able to repair this? (btw the upcoming pandas version is dumping python2 support: https://pandas.pydata.org/pandas-docs/version/0.25.0/whatsnew/v0.25.0.html). ENDQUOTE Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
-rw-r--r--academic/pyCRAC/MANIFEST_slack.txt69
-rw-r--r--academic/pyCRAC/README5
-rw-r--r--academic/pyCRAC/pyCRAC.SlackBuild2
-rw-r--r--academic/pyCRAC/pyCRAC.info8
-rw-r--r--academic/pyCRAC/setup_slack.py2
5 files changed, 9 insertions, 77 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..bcdd92ce68 100644
--- a/academic/pyCRAC/README
+++ b/academic/pyCRAC/README
@@ -26,6 +26,7 @@ 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
@@ -33,11 +34,11 @@ 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
+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
+name of the experiment.
The file containing the adapter sequences should be in the fasta format.
diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild
index bf5735f064..c1d07ea84a 100644
--- a/academic/pyCRAC/pyCRAC.SlackBuild
+++ b/academic/pyCRAC/pyCRAC.SlackBuild
@@ -23,7 +23,7 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=pyCRAC
-VERSION=${VERSION:-1.4.4}
+VERSION=${VERSION:-1.4.5}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info
index 084ba6b10a..461efdba1c 100644
--- a/academic/pyCRAC/pyCRAC.info
+++ b/academic/pyCRAC/pyCRAC.info
@@ -1,12 +1,12 @@
PRGNAM="pyCRAC"
-VERSION="1.4.4"
+VERSION="1.4.5"
HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html"
-DOWNLOAD="https://files.pythonhosted.org/packages/d2/fa/c089e3dd8640f3c8a2d37287e351e5eafc3e2855c4c83b3a213482910ac5/pyCRAC-1.4.4.tar.gz \
+DOWNLOAD="https://files.pythonhosted.org/packages/71/1b/a2aa3181af98e48fb5bf780592afe108fcfdfdcd6cf387e71d83d16390ae/pyCRAC-1.4.5.tar.gz \
https://bitbucket.org/sgrann/kinetic_crac_pipeline/get/ffe91cc6bf7a.tar.gz"
-MD5SUM="e64dd0042da31b99f24bf5af0c97f012 \
+MD5SUM="38ae4e142c31c1d641fa9f4fc6d3e40c \
8c19a15c439941cc5ae17e083f52143a"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
-REQUIRES="python3 flexbar novocraft numpy pysam scipy pandas ruffus"
+REQUIRES="python3 flexbar novocraft numpy3 pysam scipy3 pandas ruffus"
MAINTAINER="Rob van Nues"
EMAIL="sborg63@disroot.org"
diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py
index 610c4588a3..90d3b2075a 100644
--- a/academic/pyCRAC/setup_slack.py
+++ b/academic/pyCRAC/setup_slack.py
@@ -2,7 +2,7 @@
__author__ = "Sander Granneman"
__copyright__ = "Copyright 2019"
-__version__ = "1.4.4"
+__version__ = "1.4.5"
__credits__ = ["Sander Granneman","Hywell Dunn Davies"]
__maintainer__ = ["Sander Granneman","Rob van Nues via SlackBuilds.org"]
__email__ = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"]