listing git files failed - pretending there aren't any
./
install/
install/slack-desc
usr/
usr/bin/
usr/bin/CRAC_pipeline_PE.py
usr/bin/CRAC_pipeline_SE.py
usr/bin/pyAlignment2Tab.py
usr/bin/pyBarcodeFilter.py
usr/bin/pyBinCollector.py
usr/bin/pyCalculateChromosomeLengths.py
usr/bin/pyCalculateFDRs.py
usr/bin/pyCalculateMutationFrequencies.py
usr/bin/pyCheckGTFfile.py
usr/bin/pyClusterReads.py
usr/bin/pyExtractLinesFromGTF.py
usr/bin/pyFasta2tab.py
usr/bin/pyFastqDuplicateRemover.py
usr/bin/pyFastqJoiner.py
usr/bin/pyFastqSplitter.py
usr/bin/pyFilterGTF.py
usr/bin/pyGTF2bed.py
usr/bin/pyGTF2bedGraph.py
usr/bin/pyGTF2sgr.py
usr/bin/pyGetGTFSources.py
usr/bin/pyGetGeneNamesFromGTF.py
usr/bin/pyMotif.py
usr/bin/pyNormalizeIntervalLengths.py
usr/bin/pyPileup.py
usr/bin/pyReadAligner.py
usr/bin/pyReadCounters.py
usr/bin/pySelectMotifsFromGTF.py
usr/bin/pybed2GTF.py
usr/doc/
usr/doc/pyCRAC-1.5.1/
usr/doc/pyCRAC-1.5.1/README
usr/doc/pyCRAC-1.5.1/README.md
usr/doc/pyCRAC-1.5.1/README.tests
usr/doc/pyCRAC-1.5.1/The_pyCRAC_Manual.pdf
usr/doc/pyCRAC-1.5.1/crac_pipelines-README.md
usr/doc/pyCRAC-1.5.1/pyCRAC.SlackBuild
usr/doc/pyCRAC-1.5.1/setup.py.ORIG
usr/doc/pyCRAC-1.5.1/setup_slack.py
usr/lib/
usr/lib/python3.9/
usr/lib/python3.9/site-packages/
usr/lib/python3.9/site-packages/pyCRAC/
usr/lib/python3.9/site-packages/pyCRAC-1.5.1-py3.9.egg-info/
usr/lib/python3.9/site-packages/pyCRAC-1.5.1-py3.9.egg-info/PKG-INFO
usr/lib/python3.9/site-packages/pyCRAC-1.5.1-py3.9.egg-info/SOURCES.txt
usr/lib/python3.9/site-packages/pyCRAC-1.5.1-py3.9.egg-info/dependency_links.txt
usr/lib/python3.9/site-packages/pyCRAC-1.5.1-py3.9.egg-info/requires.txt
usr/lib/python3.9/site-packages/pyCRAC-1.5.1-py3.9.egg-info/top_level.txt
usr/lib/python3.9/site-packages/pyCRAC/Classes/
usr/lib/python3.9/site-packages/pyCRAC/Classes/Aligner.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/Barcodes.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/Clustering.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/Counters.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/CountsNormalization.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/Coverage.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/Exceptions.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/FDR.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/Motifs.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/NGSFormatReaders.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/NGSFormatWriters.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/PairedReads.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/Pileups.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/__init__.py
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/Aligner.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/Barcodes.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/Clustering.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/Counters.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/CountsNormalization.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/Coverage.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/Exceptions.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/FDR.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/Motifs.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/NGSFormatReaders.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/NGSFormatWriters.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/PairedReads.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/Pileups.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Classes/__pycache__/__init__.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Methods/
usr/lib/python3.9/site-packages/pyCRAC/Methods/__init__.py
usr/lib/python3.9/site-packages/pyCRAC/Methods/__pycache__/
usr/lib/python3.9/site-packages/pyCRAC/Methods/__pycache__/__init__.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Parsers/
usr/lib/python3.9/site-packages/pyCRAC/Parsers/GTF2.py
usr/lib/python3.9/site-packages/pyCRAC/Parsers/Novoalign.py
usr/lib/python3.9/site-packages/pyCRAC/Parsers/ParseAlignments.py
usr/lib/python3.9/site-packages/pyCRAC/Parsers/SAM.py
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__init__.py
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__pycache__/
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__pycache__/GTF2.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__pycache__/Novoalign.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__pycache__/ParseAlignments.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__pycache__/SAM.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__pycache__/__init__.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__pycache__/fasta2dict.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Parsers/__pycache__/tab2dict.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/Parsers/fasta2dict.py
usr/lib/python3.9/site-packages/pyCRAC/Parsers/tab2dict.py
usr/lib/python3.9/site-packages/pyCRAC/__init__.py
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/__init__.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyBarcodeFilter.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyBinCollector.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyCalculateFDRs.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyCalculateMutationFrequencies.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyClusterReads.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyMotif.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyPileup.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyReadAligner.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/__pycache__/pyReadCounters.cpython-39.pyc
usr/lib/python3.9/site-packages/pyCRAC/pyBarcodeFilter.py
usr/lib/python3.9/site-packages/pyCRAC/pyBinCollector.py
usr/lib/python3.9/site-packages/pyCRAC/pyCalculateFDRs.py
usr/lib/python3.9/site-packages/pyCRAC/pyCalculateMutationFrequencies.py
usr/lib/python3.9/site-packages/pyCRAC/pyClusterReads.py
usr/lib/python3.9/site-packages/pyCRAC/pyMotif.py
usr/lib/python3.9/site-packages/pyCRAC/pyPileup.py
usr/lib/python3.9/site-packages/pyCRAC/pyReadAligner.py
usr/lib/python3.9/site-packages/pyCRAC/pyReadCounters.py
usr/share/
usr/share/pyCRAC-1.5.1/
usr/share/pyCRAC-1.5.1/db/
usr/share/pyCRAC-1.5.1/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa
usr/share/pyCRAC-1.5.1/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
usr/share/pyCRAC-1.5.1/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
usr/share/pyCRAC-1.5.1/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
usr/share/pyCRAC-1.5.1/tests/
usr/share/pyCRAC-1.5.1/tests/barcodes.txt
usr/share/pyCRAC-1.5.1/tests/genes.list
usr/share/pyCRAC-1.5.1/tests/indexes.txt
usr/share/pyCRAC-1.5.1/tests/test.gtf
usr/share/pyCRAC-1.5.1/tests/test.novo
usr/share/pyCRAC-1.5.1/tests/test.sh
usr/share/pyCRAC-1.5.1/tests/test_coordinates.txt
usr/share/pyCRAC-1.5.1/tests/test_f.fastq
usr/share/pyCRAC-1.5.1/tests/test_f.fastq.gz
usr/share/pyCRAC-1.5.1/tests/test_f_dm.fastq
usr/share/pyCRAC-1.5.1/tests/test_r.fastq
usr/share/pyCRAC-1.5.1/tests/test_r.fastq.gz
usr/share/pyCRAC-1.5.1/tests/test_r_dm.fastq
est_code/test_single_end_run/flexbar_trimmed/
crac_pipelines-master/test_code/test_single_end_run/flexbar_trimmed/test_1_trimmed.fastq
crac_pipelines-master/test_code/test_single_end_run/log_file.txt
crac_pipelines-master/test_code/test_single_end_run/novo_files/
crac_pipelines-master/test_code/test_single_end_run/novo_files/test_1_trimmed.novo
crac_pipelines-master/test_code/test_single_end_run/pyReadCounters_analyses/
crac_pipelines-master/test_code/test_single_end_run/pyReadCounters_analyses/test_1_trimmed_count_output_reads.gtf
crac_pipelines-master/test_code/test_single_end_run/pyReadCounters_analyses/test_1_trimmed_file_statistics_reads.txt
crac_pipelines-master/test_code/test_single_end_run/pyReadCounters_analyses/test_1_trimmed_hittable_reads.txt
crac_pipelines-master/test_code/test_single_end_run/pyReadCounters_blocks_nomuts_analyses/
crac_pipelines-master/test_code/test_single_end_run/pyReadCounters_blocks_nomuts_analyses/test_1_trimmed_blocks_nomuts_count_output_cDNAs.gtf
crac_pipelines-master/test_code/test_single_end_run/pyReadCounters_blocks_nomuts_analyses/test_1_trimmed_blocks_nomuts_file_statistics_cDNAs.txt
crac_pipelines-master/test_code/test_single_end_run/pyReadCounters_blocks_nomuts_analyses/test_1_trimmed_blocks_nomuts_hittable_cDNAs.txt
crac_pipelines-master/test_data/
crac_pipelines-master/test_data/test_1.fastq
crac_pipelines-master/test_data/test_2.fastq
crac_pipelines-master/test_single_end_run/
crac_pipelines-master/test_single_end_run/log_file.txt

Installing pyCRAC version 1.5.1...
running install
running build
running build_py
creating build
creating build/lib
creating build/lib/pyCRAC
copying pyCRAC/__init__.py -> build/lib/pyCRAC
copying pyCRAC/pyBarcodeFilter.py -> build/lib/pyCRAC
copying pyCRAC/pyBinCollector.py -> build/lib/pyCRAC
copying pyCRAC/pyCalculateFDRs.py -> build/lib/pyCRAC
copying pyCRAC/pyCalculateMutationFrequencies.py -> build/lib/pyCRAC
copying pyCRAC/pyClusterReads.py -> build/lib/pyCRAC
copying pyCRAC/pyMotif.py -> build/lib/pyCRAC
copying pyCRAC/pyPileup.py -> build/lib/pyCRAC
copying pyCRAC/pyReadAligner.py -> build/lib/pyCRAC
copying pyCRAC/pyReadCounters.py -> build/lib/pyCRAC
creating build/lib/pyCRAC/Parsers
copying pyCRAC/Parsers/GTF2.py -> build/lib/pyCRAC/Parsers
copying pyCRAC/Parsers/Novoalign.py -> build/lib/pyCRAC/Parsers
copying pyCRAC/Parsers/ParseAlignments.py -> build/lib/pyCRAC/Parsers
copying pyCRAC/Parsers/SAM.py -> build/lib/pyCRAC/Parsers
copying pyCRAC/Parsers/__init__.py -> build/lib/pyCRAC/Parsers
copying pyCRAC/Parsers/fasta2dict.py -> build/lib/pyCRAC/Parsers
copying pyCRAC/Parsers/tab2dict.py -> build/lib/pyCRAC/Parsers
creating build/lib/pyCRAC/Classes
copying pyCRAC/Classes/Aligner.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/Barcodes.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/Clustering.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/Counters.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/CountsNormalization.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/Coverage.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/Exceptions.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/FDR.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/Motifs.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/NGSFormatReaders.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/NGSFormatWriters.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/PairedReads.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/Pileups.py -> build/lib/pyCRAC/Classes
copying pyCRAC/Classes/__init__.py -> build/lib/pyCRAC/Classes
creating build/lib/pyCRAC/Methods
copying pyCRAC/Methods/__init__.py -> build/lib/pyCRAC/Methods
running build_scripts
creating build/scripts-3.9
copying and adjusting pyCRAC/pyReadAligner.py -> build/scripts-3.9
copying and adjusting pyCRAC/pyMotif.py -> build/scripts-3.9
copying and adjusting pyCRAC/pyPileup.py -> build/scripts-3.9
copying and adjusting pyCRAC/pyBarcodeFilter.py -> build/scripts-3.9
copying and adjusting pyCRAC/pyReadCounters.py -> build/scripts-3.9
copying and adjusting pyCRAC/pyBinCollector.py -> build/scripts-3.9
copying and adjusting pyCRAC/pyCalculateFDRs.py -> build/scripts-3.9
copying and adjusting pyCRAC/pyClusterReads.py -> build/scripts-3.9
copying and adjusting pyCRAC/pyCalculateMutationFrequencies.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyCalculateChromosomeLengths.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyFastqDuplicateRemover.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyAlignment2Tab.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyGetGTFSources.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pySelectMotifsFromGTF.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyFasta2tab.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyFastqJoiner.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyFastqSplitter.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyExtractLinesFromGTF.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyGetGeneNamesFromGTF.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyCheckGTFfile.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pybed2GTF.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyGTF2sgr.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyGTF2bed.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyGTF2bedGraph.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyFilterGTF.py -> build/scripts-3.9
copying and adjusting pyCRAC/scripts/pyNormalizeIntervalLengths.py -> build/scripts-3.9
copying and adjusting pyCRAC/crac_pipelines/CRAC_pipeline_PE.py -> build/scripts-3.9
copying and adjusting pyCRAC/crac_pipelines/CRAC_pipeline_SE.py -> build/scripts-3.9
changing mode of build/scripts-3.9/pyReadAligner.py from 644 to 755
changing mode of build/scripts-3.9/pyMotif.py from 644 to 755
changing mode of build/scripts-3.9/pyPileup.py from 644 to 755
changing mode of build/scripts-3.9/pyBarcodeFilter.py from 644 to 755
changing mode of build/scripts-3.9/pyReadCounters.py from 644 to 755
changing mode of build/scripts-3.9/pyBinCollector.py from 644 to 755
changing mode of build/scripts-3.9/pyCalculateFDRs.py from 644 to 755
changing mode of build/scripts-3.9/pyClusterReads.py from 644 to 755
changing mode of build/scripts-3.9/pyCalculateMutationFrequencies.py from 644 to 755
changing mode of build/scripts-3.9/pyCalculateChromosomeLengths.py from 644 to 755
changing mode of build/scripts-3.9/pyFastqDuplicateRemover.py from 644 to 755
changing mode of build/scripts-3.9/pyAlignment2Tab.py from 644 to 755
changing mode of build/scripts-3.9/pyGetGTFSources.py from 644 to 755
changing mode of build/scripts-3.9/pySelectMotifsFromGTF.py from 644 to 755
changing mode of build/scripts-3.9/pyFasta2tab.py from 644 to 755
changing mode of build/scripts-3.9/pyFastqJoiner.py from 644 to 755
changing mode of build/scripts-3.9/pyFastqSplitter.py from 644 to 755
changing mode of build/scripts-3.9/pyExtractLinesFromGTF.py from 644 to 755
changing mode of build/scripts-3.9/pyGetGeneNamesFromGTF.py from 644 to 755
changing mode of build/scripts-3.9/pyCheckGTFfile.py from 644 to 755
changing mode of build/scripts-3.9/pybed2GTF.py from 644 to 755
changing mode of build/scripts-3.9/pyGTF2sgr.py from 644 to 755
changing mode of build/scripts-3.9/pyGTF2bed.py from 644 to 755
changing mode of build/scripts-3.9/pyGTF2bedGraph.py from 644 to 755
changing mode of build/scripts-3.9/pyFilterGTF.py from 644 to 755
changing mode of build/scripts-3.9/pyNormalizeIntervalLengths.py from 644 to 755
changing mode of build/scripts-3.9/CRAC_pipeline_PE.py from 644 to 755
changing mode of build/scripts-3.9/CRAC_pipeline_SE.py from 644 to 755
running install_lib
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/__init__.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyBarcodeFilter.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyBinCollector.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyCalculateFDRs.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyCalculateMutationFrequencies.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyClusterReads.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyMotif.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyPileup.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyReadAligner.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
copying build/lib/pyCRAC/pyReadCounters.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Parsers
copying build/lib/pyCRAC/Parsers/GTF2.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Parsers
copying build/lib/pyCRAC/Parsers/Novoalign.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Parsers
copying build/lib/pyCRAC/Parsers/ParseAlignments.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Parsers
copying build/lib/pyCRAC/Parsers/SAM.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Parsers
copying build/lib/pyCRAC/Parsers/__init__.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Parsers
copying build/lib/pyCRAC/Parsers/fasta2dict.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Parsers
copying build/lib/pyCRAC/Parsers/tab2dict.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Parsers
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/Aligner.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/Barcodes.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/Clustering.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/Counters.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/CountsNormalization.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/Coverage.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/Exceptions.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/FDR.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/Motifs.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/NGSFormatReaders.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/NGSFormatWriters.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/PairedReads.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/Pileups.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
copying build/lib/pyCRAC/Classes/__init__.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Methods
copying build/lib/pyCRAC/Methods/__init__.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Methods
byte-compiling /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/__init__.py to __init__.cpython-39.pyc
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byte-compiling /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes/Coverage.py to Coverage.cpython-39.pyc
byte-compiling /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes/Exceptions.py to Exceptions.cpython-39.pyc
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byte-compiling /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC/Classes/PairedReads.py to PairedReads.cpython-39.pyc
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running install_data
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share
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creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/db
copying pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/db/
copying pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/db/
copying pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/db/
copying pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/db/
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests
copying tests/test.novo -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
copying tests/test.sh -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
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copying tests/test.gtf -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
copying tests/test_f.fastq -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
copying tests/test_f.fastq.gz -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
copying tests/test_f_dm.fastq -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
copying tests/test_r.fastq -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
copying tests/test_r.fastq.gz -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
copying tests/test_r_dm.fastq -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
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copying tests/barcodes.txt -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
copying tests/genes.list -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/share/pyCRAC-1.5.1/tests/
running install_egg_info
running egg_info
writing pyCRAC.egg-info/PKG-INFO
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reading manifest file 'pyCRAC.egg-info/SOURCES.txt'
writing manifest file 'pyCRAC.egg-info/SOURCES.txt'
Copying pyCRAC.egg-info to /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/lib/python3.9/site-packages/pyCRAC-1.5.1-py3.9.egg-info
running install_scripts
creating /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyReadAligner.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyMotif.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyPileup.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyBarcodeFilter.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyReadCounters.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyBinCollector.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyCalculateFDRs.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
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copying build/scripts-3.9/pyCalculateMutationFrequencies.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyCalculateChromosomeLengths.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyFastqDuplicateRemover.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyAlignment2Tab.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyGetGTFSources.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pySelectMotifsFromGTF.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyFasta2tab.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
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copying build/scripts-3.9/pyFastqSplitter.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyExtractLinesFromGTF.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyGetGeneNamesFromGTF.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyCheckGTFfile.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pybed2GTF.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyGTF2sgr.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
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copying build/scripts-3.9/pyFilterGTF.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/pyNormalizeIntervalLengths.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
copying build/scripts-3.9/CRAC_pipeline_PE.py -> /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin
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changing mode of /usr/src/slapt-src/academic/pyCRAC/package-pyCRAC/usr/bin/pyReadCounters.py to 755
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Slackware package maker, version 3.14159265.

Searching for symbolic links:

No symbolic links were found, so we won't make an installation script.
You can make your own later in ./install/doinst.sh and rebuild the
package if you like.

This next step is optional - you can set the directories in your package
to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

Would you like to reset all directory permissions to 755 (drwxr-xr-x) and
directory ownerships to root.root ([y]es, [n]o)? n

Creating Slackware package:  /usr/src/slapt-src/academic/pyCRAC/pyCRAC-1.5.1-i586-1salix15.0.txz

WARNING:  zero length file usr/lib/python3.9/site-packages/pyCRAC/Parsers/__init__.py
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Slackware package /usr/src/slapt-src/academic/pyCRAC/pyCRAC-1.5.1-i586-1salix15.0.txz created.

Installing package pyCRAC-1.5.1-i586-1salix15.0...
| pyCRAC (Next generation sequencing analysis with Python)
| 
| pyCRAC combines cross-linking and immunoprecipitation (CLIP)/
| cross-linking and cDNA analysis (CRAC) analysis methods.
| It can be used to remove duplicate reads, tackles directional
| libraries and reports sense and anti-sense hits.
| 
| Included is a pipeline that allows analysis of a group of data-sets.
| 
| https://bitbucket.org/sgrann/
| 
| 
|