# HG changeset patch
# User ieguinoa
# Date 1621955696 0
# Node ID e23440b3332a361db1ea42c0c4a58d3a2dcd8887
Uploaded
diff -r 000000000000 -r e23440b3332a data_manager/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,248 @@
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+ 2.7.8a
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+ 2.7.4a
+ rnastar_index2x_versioned
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+ star
+ samtools
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+ topic_3170
+ topic_3308
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+ operation_0292
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+ --readFilesCommand zcat
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+ 10.1093/bioinformatics/bts635
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diff -r 000000000000 -r e23440b3332a data_manager/rna_star_index_builder.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/rna_star_index_builder.py Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--config-file')
+ parser.add_argument('--value')
+ parser.add_argument('--dbkey')
+ parser.add_argument('--name')
+ parser.add_argument('--subdir')
+ parser.add_argument('--data-table')
+ parser.add_argument('--with-gene-model', action='store_true')
+ parser.add_argument('--index-version')
+
+ args = parser.parse_args()
+
+ if args.dbkey in [None, '', '?']:
+ raise Exception(
+ '"%s" is not a valid dbkey. You must specify a valid dbkey.'
+ % (args.dbkey)
+ )
+
+ with_gene_model = "0"
+ if args.with_gene_model:
+ with_gene_model = "1"
+
+ data_manager_dict = {
+ 'data_tables': {
+ args.data_table: [
+ {
+ "value": args.value,
+ "dbkey": args.dbkey,
+ "name": args.name,
+ "path": args.subdir,
+ "with_gene_model": with_gene_model,
+ "version": args.index_version
+ }
+ ]
+ }
+ }
+ with open(args.config_file, 'w') as fh:
+ json.dump(data_manager_dict, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r e23440b3332a data_manager/rna_star_index_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/rna_star_index_builder.xml Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,183 @@
+
+ builder
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+ macros.xml
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+ python
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+ --seedSearchStartLmax.
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+ Cheers
+ Alex
+
+*Note on gene model requirements for splice junctions*
+
+From https://groups.google.com/forum/#!msg/rna-star/3Y_aaTuzBrE/lUylTB8h5vMJ::
+
+ When you generate a genome with annotations, you need to specify --sjdbOverhang value, which ideally should be equal to (oneMateLength-1), or you could use a generic value of ~100.
+
+ Your gtf lines look fine to me. STAR needs 3 features from a GTF file:
+ 1. Chromosome names in col.1 that agree with chromosome names in genome .fasta files. If you have "chr2L" names in the genome .fasta files, and "2L" in the .gtf file, then you need to use --sjdbGTFchrPrefix chr option.
+ 2. 'exon' in col.3 for the exons of all transcripts (this name can be changed with --sjdbGTFfeatureExon)
+ 3. 'transcript_id' attribute that assigns each exon to a transcript (--this name can be changed with --sjdbGTFtagExonParentTranscript)
+
+ Cheers
+ Alex
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+ ]]>
+
+
diff -r 000000000000 -r e23440b3332a data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,25 @@
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diff -r 000000000000 -r e23440b3332a test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,19 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
+phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta
diff -r 000000000000 -r e23440b3332a test-data/phiX174.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+
diff -r 000000000000 -r e23440b3332a test-data/rnastar_index2_versioned.loc
diff -r 000000000000 -r e23440b3332a test-data/test_star_01.data_manager_json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_star_01.data_manager_json Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"rnastar_index2x_versioned": \[{"dbkey": "phiX174", "name": "phiX174", "path": ".*", "value": "phiX174", "version": "2.7.4a", "with_gene_model": "0"}\]}}
diff -r 000000000000 -r e23440b3332a tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r e23440b3332a tool-data/rnastar_index2x_versioned.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rnastar_index2x_versioned.loc.sample Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,27 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of rna-star indexed sequences data files.
+#You will need to create these data files and then create a
+#rnastar_index2x_versioned.loc file similar to this one (store it in this
+directory) that points to the directories in which those files are stored.
+#The rnastar_index2x_versioned.loc file has this format (longer white space
+#characters are TAB characters):
+#
+#
+#
+#The column should be 1 or 0, indicating whether the index
+#was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
+#or not.
+#
+#The column indicates the STAR version that introduced the format of
+#the index, i.e., the oldest STAR version that could make use of the index.
+#
+#Note that STAR indices can become quite large. Consequently, it is only
+#advisable to create indices with annotations if it's known ahead of time that
+#(A) the annotations won't be frequently updated and (B) the read lengths used
+#will also rarely vary. If either of these is not the case, it's advisable to
+#create indices without annotations and then specify an annotation file and
+#maximum read length (minus 1) when running STAR.
+#
+#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a
+#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a
+
diff -r 000000000000 -r e23440b3332a tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue May 25 15:14:56 2021 +0000
@@ -0,0 +1,12 @@
+
+
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+ value, dbkey, name, path
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+ value, dbkey, name, path, with_gene_model, version
+
+