Mercurial > repos > iuc > gatk4_mutect2

annotate tool-data/all_fasta.loc.sample @ 7:91d37702c47b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 commit 301f94b20e29da22d5f4502c44344f4a0115930d
author iuc
date Wed, 24 Aug 2022 17:58:18 +0000
parents 269335b7ff6e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
2 #under the "genome" directory (a directory that contains a directory
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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5 #TAB characters):
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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6 #
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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8 #
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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9 #So, all_fasta.loc could look something like this:
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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10 #
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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14 #
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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17 #such as with hg19 above.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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18 #