annotate tool-data/all_fasta.loc.sample @ 0:460f0749aac5 draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
author yhoogstrate
date Thu, 05 Nov 2015 07:49:02 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
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1 #This file lists the locations and dbkeys of all the fasta files
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
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diff changeset
2 #under the "genome" directory (a directory that contains a directory
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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3 #for each build). The script extract_fasta.py will generate the file
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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5 #TAB characters):
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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6 #
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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8 #
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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9 #So, all_fasta.loc could look something like this:
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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10 #
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
14 #
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
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16 #fasta file. So there will be multiple fasta files for each build,
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
17 #such as with hg19 above.
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
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18 #