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Merge pull request #57 from tgen/develop
Supports releases v1.2.x
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| # Mouse Pipeline | ||
| # Mouse Pipeline supports mm10 mouse genome with ensembl 98 gene models | ||
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| ### This directory contains Automated scripts for building files need for cactusMouse pipeline | ||
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| # ../shared_resource_creation_scripts/create_genome_reference.sh cactusMouse_resources.ini | ||
| # ../shared_resource_creation_scripts/create_bwa_genome_index_cactusMouse.sh cactusMouse_resources.ini | ||
| # ../shared_resource_creation_scripts/create_gene_model.sh cactusMouse_resources.ini | ||
| # ../shared_resource_creation_scripts/create_star_genome_index_catcusMouse.sh cactusMouse_resources.ini /home/kdrenner/jetstream_resources/cactusMouse/star_index_lengths.csv | ||
| ##### Had to update the create_star_genome_index.sh file. Received the error that not enough RAM was allocated. | ||
| #### Used --limitGenomeGenerateRAM 34000000000 and the code was able to run | ||
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| # ../shared_resource_creation_scripts/create_salmon_index.sh cactusMouse_resources.ini | ||
| # ../shared_resource_creation_scripts/create_snpEff_db.sh cactusMouse_resources.ini | ||
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| supports mm10 mouse genome with ensembl xx gene models |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| SC2,Agilent_SureSelect_Canine_Exon_V2,agilent_canine_exonV2_targets_sorted.bed,agilent_canine_exonV2_targets_sorted.bed | ||
| XT2,Agilent_SureSelect_XT2_Vidium_v1.0,Vidium_v1.0_exome_Covered_nochr_noheader.bed,Vidium_v1.0_exome_Covered_nochr_noheader.bed |
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| #!/usr/bin/env bash | ||
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| ### Setting as an interactive BASH session and forcing history to capture commands to a log/README file | ||
| HISTFILE=~/.bash_history | ||
| set -o history | ||
| set -ue | ||
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| # Read required variables from configuration file | ||
| . ${1} | ||
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| #################################### | ||
| ## Navigate Directory Structure | ||
| ################################### | ||
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| # Check top level directory if not available | ||
| if [ -e ${TOPLEVEL_DIR} ] | ||
| then | ||
| echo "Top level directory: ${TOPLEVEL_DIR} exists, moving into it" | ||
| cd ${TOPLEVEL_DIR} | ||
| else | ||
| echo "Top level directory NOT found, IT IS REQUIRED, EXITING" | ||
| exit 1 | ||
| fi | ||
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| # Check that the reference genome was created successfully | ||
| if [ -e GENOME_FASTA_GENERATION_COMPLETE ] | ||
| then | ||
| echo "Genome fasta exists, moving forward" | ||
| else | ||
| echo "Genome fasta generation complete flag NOT found" | ||
| echo "Try again later as this is required" | ||
| exit 2 | ||
| fi | ||
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| #################################### | ||
| ## Generate BWA index | ||
| #################################### | ||
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| if [ -e tool_resources ] | ||
| then | ||
| echo "tool_resources directory exists, moving into it" | ||
| cd tool_resources | ||
| else | ||
| echo "tool_resources directory NOT found, creating and moving into it now" | ||
| mkdir tool_resources | ||
| cd tool_resources | ||
| fi | ||
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| if [ -e "samtools_stats" ] | ||
| then | ||
| echo "The samtools_stats directory exists, exiting to prevent overwriting existing non_N_region_file." | ||
| exit 2 | ||
| else | ||
| echo "The samtools_stats directory was NOT found, creating and moving into it now" | ||
| mkdir samtools_stats | ||
| cd samtools_stats | ||
| fi | ||
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| # Initialize a samtools_stats index README | ||
| touch README | ||
| echo >> README | ||
| echo "For details on file creation see the associated github repository:" >> README | ||
| echo "https://github.com/tgen/jetstream_resources/coyote" >> README | ||
| echo "Created and downloaded by ${CREATOR}" >> README | ||
| date >> README | ||
| echo >> README | ||
| echo "samtools stats --target-regions non_N_region_file creation details:" >> README | ||
| echo >> README | ||
| echo "By default samtools stats consideres all bases, including N's, in the reference genome when calculating stats." > README | ||
| echo "The 1 based regions file generated by make_samtools_stats_non_N_region_file_from_fasta.awk excludes all N bases" > README | ||
| echo "and is passed to the --target-regions option of samtools stats to ensure coverage and mapping statistics are " >> README | ||
| echo "calculated based on non N genome space." >> README | ||
| echo >> README | ||
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| # Create bwa index files using bwa utility script | ||
| echo "Create samtools stats non N region file of primary contigs with chrX removed as follows:" >> README | ||
| sbatch --export ALL ${PATH_TO_REPO}/utility_scripts/make_samtools_stats_non_N_region_file_from_fasta.awk ${REFERENCE_DNA_GENOME_FASTA} canfam3.1_coyote_samstats_no_N_1based_primary_contigs_no_chrX.txt 1CONTIG_SEP2CONTIG_SEP3CONTIG_SEP4CONTIG_SEP5CONTIG_SEP6CONTIG_SEP7CONTIG_SEP8CONTIG_SEP9CONTIG_SEP10CONTIG_SEP11CONTIG_SEP12CONTIG_SEP13CONTIG_SEP14CONTIG_SEP15CONTIG_SEP16CONTIG_SEP17CONTIG_SEP18CONTIG_SEP19CONTIG_SEP20CONTIG_SEP21CONTIG_SEP22CONTIG_SEP23CONTIG_SEP24CONTIG_SEP25CONTIG_SEP26CONTIG_SEP27CONTIG_SEP28CONTIG_SEP29CONTIG_SEP30CONTIG_SEP31CONTIG_SEP32CONTIG_SEP33CONTIG_SEP34CONTIG_SEP35CONTIG_SEP36CONTIG_SEP37CONTIG_SEP38 | ||
| fc -ln -1 >> README | ||
| echo >> README | ||
| cat ${PATH_TO_REPO}/utility_scripts/make_samtools_stats_non_N_region_file_from_fasta.awk >> README | ||
| echo >> README | ||
| echo >> README |
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