./
install/
install/doinst.sh
install/slack-desc
usr/
usr/bin/
usr/doc/
usr/doc/snpEff-4.3t/
usr/doc/snpEff-4.3t/References
usr/doc/snpEff-4.3t/snpEff.SlackBuild
usr/share/
usr/share/java/
usr/share/java/snpEff/
usr/share/java/snpEff/SnpSift.jar
usr/share/java/snpEff/examples/
usr/share/java/snpEff/examples/1kg.head_chr1.filtered.vcf.gz
usr/share/java/snpEff/examples/1kg.head_chr1.vcf.gz
usr/share/java/snpEff/examples/cancer.ann.vcf
usr/share/java/snpEff/examples/cancer.eff.vcf
usr/share/java/snpEff/examples/cancer.vcf
usr/share/java/snpEff/examples/cancer_pedigree.ann.vcf
usr/share/java/snpEff/examples/cancer_pedigree.vcf
usr/share/java/snpEff/examples/example_motif.vcf
usr/share/java/snpEff/examples/examples.sh
usr/share/java/snpEff/examples/file.vcf
usr/share/java/snpEff/examples/intervals.bed
usr/share/java/snpEff/examples/my_annotations.bed
usr/share/java/snpEff/examples/samples_cancer.txt
usr/share/java/snpEff/examples/samples_cancer_one.txt
usr/share/java/snpEff/examples/test.1KG.ann_encode.vcf
usr/share/java/snpEff/examples/test.1KG.ann_reg.vcf
usr/share/java/snpEff/examples/test.1KG.vcf
usr/share/java/snpEff/examples/test.ann.vcf
usr/share/java/snpEff/examples/test.chr22.ann.filter_missense.vcf
usr/share/java/snpEff/examples/test.chr22.ann.filter_missense_any.vcf
usr/share/java/snpEff/examples/test.chr22.ann.filter_missense_any_TRMT2A.vcf
usr/share/java/snpEff/examples/test.chr22.ann.filter_missense_first.vcf
usr/share/java/snpEff/examples/test.chr22.ann.one_per_line.txt
usr/share/java/snpEff/examples/test.chr22.ann.txt
usr/share/java/snpEff/examples/test.chr22.ann.vcf
usr/share/java/snpEff/examples/test.chr22.vcf
usr/share/java/snpEff/examples/test.vcf
usr/share/java/snpEff/examples/variants_1.ann.vcf
usr/share/java/snpEff/examples/variants_1.vcf
usr/share/java/snpEff/examples/variants_2.ann.vcf
usr/share/java/snpEff/examples/variants_2.vcf
usr/share/java/snpEff/galaxy/
usr/share/java/snpEff/galaxy/snpEff.xml
usr/share/java/snpEff/galaxy/snpEffWrapper.pl
usr/share/java/snpEff/galaxy/snpEff_download.xml
usr/share/java/snpEff/galaxy/snpSiftWrapper.pl
usr/share/java/snpEff/galaxy/snpSift_annotate.xml
usr/share/java/snpEff/galaxy/snpSift_caseControl.xml
usr/share/java/snpEff/galaxy/snpSift_filter.xml
usr/share/java/snpEff/galaxy/snpSift_int.xml
usr/share/java/snpEff/galaxy/tool-data/
usr/share/java/snpEff/galaxy/tool-data/snpEff_genomes.loc
usr/share/java/snpEff/galaxy/tool-data/snpEff_genomes.loc.sample
usr/share/java/snpEff/galaxy/tool_conf.xml
usr/share/java/snpEff/galaxy/tool_dependencies.xml
usr/share/java/snpEff/scripts/
usr/share/java/snpEff/scripts/1kg.sh
usr/share/java/snpEff/scripts/annotate_demo.sh
usr/share/java/snpEff/scripts/annotate_demo_GATK.sh
usr/share/java/snpEff/scripts/bedEffOnePerLine.pl
usr/share/java/snpEff/scripts/buildDbNcbi.sh
usr/share/java/snpEff/scripts/cgShore.pl
usr/share/java/snpEff/scripts/cgShore.sh
usr/share/java/snpEff/scripts/countColumns.py
usr/share/java/snpEff/scripts/db.pl
usr/share/java/snpEff/scripts/extractSequences.pl
usr/share/java/snpEff/scripts/fasta2tab.pl
usr/share/java/snpEff/scripts/fastaSample.pl
usr/share/java/snpEff/scripts/fastaSplit.pl
usr/share/java/snpEff/scripts/fastqSplit.pl
usr/share/java/snpEff/scripts/filterBy.py
usr/share/java/snpEff/scripts/gffRemovePhase.pl
usr/share/java/snpEff/scripts/gsa/
usr/share/java/snpEff/scripts/gsa/bayesFactor_correction_scoreCount.r
usr/share/java/snpEff/scripts/gsa/bayesFactor_correction_scoreCount.sh
usr/share/java/snpEff/scripts/gsa/bayesFactor_correction_scoreCount_max10.sh
usr/share/java/snpEff/scripts/gsa/checkGeneNames.py
usr/share/java/snpEff/scripts/gsa/create_sets.bds
usr/share/java/snpEff/scripts/gsa/geneSetOverlap.py
usr/share/java/snpEff/scripts/gsa/geneSetOverlap.sort.txt
usr/share/java/snpEff/scripts/gsa/geneSetsGtex.py
usr/share/java/snpEff/scripts/gsa/pvalue_correction_scoreCount.r
usr/share/java/snpEff/scripts/gsa/pvalue_correction_scoreCount.sh
usr/share/java/snpEff/scripts/gsa/pvalue_correction_scoreCount_min10.sh
usr/share/java/snpEff/scripts/isutf8.py
usr/share/java/snpEff/scripts/join.pl
usr/share/java/snpEff/scripts/joinSnpEff.pl
usr/share/java/snpEff/scripts/make_dbNSFP.sh
usr/share/java/snpEff/scripts/nextProt_filter.pl
usr/share/java/snpEff/scripts/ped2vcf.py
usr/share/java/snpEff/scripts/plot.pl
usr/share/java/snpEff/scripts/plotHistogram.pl
usr/share/java/snpEff/scripts/plotLabel.pl
usr/share/java/snpEff/scripts/plotMA.pl
usr/share/java/snpEff/scripts/plotQQ.pl
usr/share/java/snpEff/scripts/plotQQsubsample.pl
usr/share/java/snpEff/scripts/plotSmoothScatter.pl
usr/share/java/snpEff/scripts/plotXY.pl
usr/share/java/snpEff/scripts/queue.pl
usr/share/java/snpEff/scripts/sam2fastq.pl
usr/share/java/snpEff/scripts/snpEff
usr/share/java/snpEff/scripts/snpSift_filter_sample_to_number.pl
usr/share/java/snpEff/scripts/sortLine.py
usr/share/java/snpEff/scripts/splitChr.pl
usr/share/java/snpEff/scripts/statsNum.pl
usr/share/java/snpEff/scripts/swapCols.pl
usr/share/java/snpEff/scripts/transpose.pl
usr/share/java/snpEff/scripts/txt2fa.pl
usr/share/java/snpEff/scripts/txt2vcf.py
usr/share/java/snpEff/scripts/uniqCount.pl
usr/share/java/snpEff/scripts/uniqCut.pl
usr/share/java/snpEff/scripts/vcfAnnFirst.py
usr/share/java/snpEff/scripts/vcfBareBones.pl
usr/share/java/snpEff/scripts/vcfEffHighest.ORI.py
usr/share/java/snpEff/scripts/vcfEffOnePerLine.pl
usr/share/java/snpEff/scripts/vcfFilterSamples.pl
usr/share/java/snpEff/scripts/vcfInfoOnePerLine.pl
usr/share/java/snpEff/scripts/vcfOnlyAlts.pl
usr/share/java/snpEff/scripts/vcfReduceGenotypes.pl
usr/share/java/snpEff/scripts/vcfRefCorrect.py
usr/share/java/snpEff/scripts/wigSplit.pl
usr/share/java/snpEff/snpEff.config
usr/share/java/snpEff/snpEff.jar
s_1.vcf  
  inflating: snpEff/examples/example_motif.vcf  
  inflating: snpEff/examples/cancer_pedigree.ann.vcf  
  inflating: snpEff/examples/test.1KG.ann_encode.vcf  
  inflating: snpEff/examples/file.vcf  
  inflating: snpEff/examples/variants_2.ann.vcf  
  inflating: snpEff/examples/test.1KG.ann_reg.vcf  
   creating: clinEff/
  inflating: clinEff/clinEff.config  
  inflating: clinEff/ClinEff.jar     
  inflating: clinEff/workflow.config  
   creating: clinEff/workflow/
  inflating: clinEff/workflow/workflow.config  
  inflating: clinEff/workflow/workflow.GRCh38.config  
   creating: clinEff/report/
   creating: clinEff/report/bootstrap/
  inflating: clinEff/report/bootstrap/bootstrap.min.js  
  inflating: clinEff/report/bootstrap/bootstrap.min.css  
  inflating: clinEff/report/reportlof.html.flt  
  inflating: clinEff/report/reportclinical.html.flt  
  inflating: clinEff/report/style.css  
   creating: clinEff/report/img/
  inflating: clinEff/report/img/logo.png  
  inflating: clinEff/report/img/logo_example_ori.png  
 extracting: clinEff/report/img/logo_example.png  
  inflating: clinEff/report/reporthighimpact.html.flt  
/usr/src/slapt-src/academic/snpEff/snpEff

Slackware package maker, version 3.14159265.

Searching for symbolic links:
usr/bin/SnpSift.jar	../share/java/snpEff/SnpSift.jar
usr/bin/snpEff.jar	../share/java/snpEff/snpEff.jar

Making symbolic link creation script:
( cd usr/bin ; rm -rf SnpSift.jar )
( cd usr/bin ; ln -sf ../share/java/snpEff/SnpSift.jar SnpSift.jar )
( cd usr/bin ; rm -rf snpEff.jar )
( cd usr/bin ; ln -sf ../share/java/snpEff/snpEff.jar snpEff.jar )

It is recommended that you make these lines your new installation script.

Would you like to make this stuff the install script for this package
and remove the symbolic links ([y]es, [n]o)? y


Removing symbolic links:
removed './usr/bin/snpEff.jar'
removed './usr/bin/SnpSift.jar'

Creating your new ./install/doinst.sh...

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/snpEff/snpEff-4.3t-noarch-1salix15.0.txz


Slackware package /usr/src/slapt-src/academic/snpEff/snpEff-4.3t-noarch-1salix15.0.txz created.

Installing package snpEff-4.3t-noarch-1salix15.0...
| snpEff (Genetic variant annotation and effect prediction toolbox)
| 
| SnpEff is a variant annotation and effect prediction tool. It
| annotates and predicts the effects of variants on genes (such
| as amino acid changes).
| 
| Home: http://snpeff.sourceforge.net/
| 
| 
| 
| 
| 
|