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diff --git a/academic/pyCRAC/test_slack.sh b/academic/pyCRAC/test_slack.sh
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+#!/usr/bin/env bash
+echo
+echo "##### testing all pyCRAC tools #####"
+echo
+echo "# pyBarcodeFilter.py..."
+echo "...demultiplexing illumina indexes"
+pyBarcodeFilter.py -f test_f.fastq -r test_r.fastq -b indexes.txt -i -m 1
+echo "...demultiplexing illumina indexes on compressed files"
+pyBarcodeFilter.py -f test_f.fastq.gz -r test_r.fastq.gz -b indexes.txt -i -m 1 --file_type=fastq.gz
+echo "...demultiplexing random barcodes in 5' adapter"
+pyBarcodeFilter.py -f test_f_dm.fastq -r test_r_dm.fastq -b barcodes.txt -m 1
+echo "...demultiplexing random barcodes in 5' adapter on compressed data and compressing output files"
+pyBarcodeFilter.py -f test_f_dm.fastq -r test_r_dm.fastq -b barcodes.txt -m 1 --gz
+echo "# pyReadCounters..."
+echo "...range 300 and deletions only"
+pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "...same as above but counting hits for introns only"
+pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -a protein_coding --hittable -s intron -o test_intron -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "...same as above but now counting hits in exons only"
+pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -a protein_coding --hittable -s exon -o test_exon -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "# pyClusterReads..."
+pyClusterReads.py -f test_count_output_reads.gtf -r 300 --cic=5 --ch=5 --co=5 --mutsfreq=10 -o test_count_output_clusters.gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "...counting overlap between clusters and genomic features"
+pyReadCounters.py -f test_count_output_clusters.gtf --file_type=gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "# pyMotif..."
+echo "...with range setting"
+pyMotif.py -f test_count_output_clusters.gtf -r 300 -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
+echo "...with annotation = protein_coding"
+pyMotif.py -f test_count_output_clusters.gtf -a protein_coding -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
+echo "# pyBinCollector..."
+echo "...with annotation = protein_coding"
+pyBinCollector.py -f test_count_output_clusters.gtf -a protein_coding -n 50 -o test_count_output_protein_coding_50.pileup -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "...with all annotations"
+pyBinCollector.py -f test_count_output_clusters.gtf -n 50 -o test_count_output_all_50.pileup -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "...with --binoverlap flag"
+pyBinCollector.py -f test_count_output_clusters.gtf -n 50 --binoverlap 1 5 -o test_count_output_selected_1_5.gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "...with --outputall flag"
+pyBinCollector.py -f test_count_output_clusters.gtf -n 50 --outputall -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "# pyPileup..."
+echo "...with genes list"
+pyPileup.py -f test.novo -g genes.list --limit=1000 --discarded=pyPileup_discarded.txt -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
+echo "...with genes list and removal of duplicates"
+pyPileup.py -f test.novo -g genes.list --limit=1000 --blocks -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
+echo "...with chromosome coordinates"
+pyPileup.py -f test.novo --chr test_coordinates.txt --limit=1000 -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
+echo "...with chromosome coordinates and removal of duplicates"
+pyPileup.py -f test.novo --chr test_coordinates.txt --limit=1000 --blocks -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
+echo "# pyReadAligner..."
+echo "...with chromosome coordinates"
+pyReadAligner.py -f test.novo --chr test_coordinates.txt --limit=1000 --discarded=pyReadAligner_discarded.txt -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
+echo "...with genes list and mutation filtering"
+pyReadAligner.py -f test.novo -g genes.list --limit=500 --mutations=delsonly -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
+echo "# pyCalculateFDRs..."
+pyCalculateFDRs.py -f test_count_output_reads.gtf -r 200 -o test_count_output_FDRs_005.gtf -v -m 0.05 --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "# pyCalculateMutationFrequencies..."
+pyCalculateMutationFrequencies.py -i test_count_output_FDRs_005.gtf -r test_count_output_reads.gtf -o test_count_output_FDRs_005_with_muts.gtf --mutsfreq=20 -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo
+echo "##### testing pyCRAC scripts #####"
+echo
+echo "# pyFastqJoiner.py..."
+pyFastqJoiner.py -f test_f.fastq test_r.fastq -c "|" -o test_joined.fastq
+echo "...with compressed data and output compression"
+pyFastqJoiner.py -f test_f.fastq.gz test_r.fastq.gz --file_type=fastq.gz -c "|" --gz -o test_joined_compressed.fastq
+echo "...with reverse-complementing the reverse read"
+pyFastqJoiner.py -f test_f.fastq test_r.fastq --reversecomplement -c "|" -o test_reverse_joined.fastq
+echo "# pyFastqDuplicateRemover.py..."
+echo "...with single-end data"
+pyFastqDuplicateRemover.py -f test_f.fastq -o test_f.fasta
+echo "...with paired-end data"
+pyFastqDuplicateRemover.py -f test_f.fastq -r test_r.fastq -o test
+echo "# pyFastqSplitter.py..."
+pyFastqSplitter.py -f test_joined.fastq -c "|" -o test_splitted
+echo "...with compressed data"
+pyFastqSplitter.py -f test_joined_compressed.fastq.gz --file_type=fastq.gz -c "|" -o test_compressed_splitted
+echo "...with compressed data and compressing output"
+pyFastqSplitter.py -f test_joined_compressed.fastq.gz --file_type=fastq.gz -c "|" -o test_compressed_splitted --gzip
+echo "# pyCheckGTFfile.py..."
+pyCheckGTFfile.py --gtf=test.gtf -o test_corrected.gtf
+echo "# pyGetGTFSources.py..."
+pyGetGTFSources.py --gtf=test.gtf -o test_gtf_sources.txt --count
+echo "# pyGetGeneNamesFromGTF.py..."
+pyGetGeneNamesFromGTF.py --gtf=test.gtf -a gene_name -o test_gtf_gene_names.txt --count
+echo "# pyNormalizeIntervalLengths with various flags..."
+pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --fixed 20 -o test_count_output_FDRs_fixed_20.gtf -v
+pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --min 20 -o test_count_output_FDRs_min_20.gtf -v
+pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addboth 20 -o test_count_output_FDRs_addboth_20.gtf -v
+pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addleft 20 -o test_count_output_FDRs_addleft_20.gtf -v
+pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addright 20 -o test_count_output_FDRs_addright_20.gtf -v
+echo "# pyAlignment2Tab.py..."
+pyAlignment2Tab.py -f sense-reads_SNR17A_genomic_test.fasta -o sense-reads_SNR17A_genomic_test.tab
+echo "# pyExtractLinesFromGTF.py..."
+pyExtractLinesFromGTF.py --gtf=test.gtf -g genes.list -o test_snR17A.gtf -a gene_name
+echo "# pyGTF2bed.py..."
+pyGTF2bed.py --gtf=test_count_output_reads.gtf -o test.bed -n test_gtf -d test_gtf --color red
+echo "# pyGTF2bedGraph.py..."
+echo "...default settings"
+pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out -t reads -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "...normalized to hits per million"
+pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm --permillion -t reads -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "...start positions"
+pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm_5end --permillion -t startpositions -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "...end positions"
+pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm_3end --permillion -t endpositions -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "# pyGTF2sgr.py..."
+echo "...default settings"
+pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "...normalized to hits per million"
+pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm --permillion -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "...start positions"
+pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm_5end --permillion -t startpositions -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "...end positions"
+pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm_3end --permillion -t endpositions -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
+echo "# pyFilterGTF.py..."
+pyFilterGTF.py -f test_count_output_reads.gtf -o test_sense_filtered_reads.gtf -a protein_coding --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "# pybed2GTF.py..."
+pybed2GTF.py --bed=test.bed -o test_bed2gtf.gtf --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
+echo "# pyFasta2tab.py..."
+pyFasta2tab.py -f sense-reads_SNR17A_genomic_test.fasta -o sense-reads_SNR17A_genomic_test_f2a.tab
+echo
+echo "##### tests finished #####"
+echo