# HG changeset patch
# User ryanmorin
# Date 1318977127 14400
# Node ID 361d6506850aa3d44968a406a8d0eaf89670e7f2
# Parent a4975ec3457524dcce248541a88621c6f5e03674
Uploaded
diff -r a4975ec34575 -r 361d6506850a Galaxy-Workflow-Genome_Exome_paired_analysis_(SNVMix1).ga
--- a/Galaxy-Workflow-Genome_Exome_paired_analysis_(SNVMix1).ga Mon Oct 17 14:57:09 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,450 +0,0 @@
-{
- "a_galaxy_workflow": "true",
- "annotation": "",
- "format-version": "0.1",
- "name": "Genome/Exome paired analysis (SNVMix1)",
- "steps": {
- "0": {
- "annotation": "",
- "id": 0,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "Tumour bam file (rmdup or dups flagged)"
- }
- ],
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 205,
- "top": 458
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"Tumour bam file (rmdup or dups flagged)\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": []
- },
- "1": {
- "annotation": "",
- "id": 1,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "Codon resource (codon_lookup_new.sort)"
- }
- ],
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 205,
- "top": 524
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"Codon resource (codon_lookup_new.sort)\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": []
- },
- "2": {
- "annotation": "",
- "id": 2,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "SNP resource (all_known_snps.txt.current)"
- }
- ],
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 204,
- "top": 588
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"SNP resource (all_known_snps.txt.current)\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": []
- },
- "3": {
- "annotation": "",
- "id": 3,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "Normal bam file (rmdup or dups flagged)"
- }
- ],
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 205,
- "top": 652
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"Normal bam file (rmdup or dups flagged)\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": []
- },
- "4": {
- "annotation": "",
- "id": 4,
- "input_connections": {
- "refOrHistory|input1": {
- "id": 0,
- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "SNVMix",
- "outputs": [
- {
- "name": "output_snvmix",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 265.5,
- "top": 333.5
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "snvmix",
- "tool_state": "{\"q\": \"\\\"19\\\"\", \"positionFile\": \"{\\\"positions\\\": \\\"no\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"refOrHistory\": \"{\\\"input1\\\": null, \\\"reference\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"keep_dups\": \"\\\"no\\\"\", \"Q\": \"\\\"19\\\"\", \"full\": \"\\\"no\\\"\", \"keep_chastity\": \"\\\"no\\\"\", \"type\": \"\\\"SNVMix1\\\"\"}",
- "tool_version": "0.12.1-rc1",
- "type": "tool",
- "user_outputs": []
- },
- "5": {
- "annotation": "",
- "id": 5,
- "input_connections": {
- "input1": {
- "id": 4,
- "output_name": "output_snvmix"
- }
- },
- "inputs": [],
- "name": "SNVMix filter",
- "outputs": [
- {
- "name": "output1",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 554,
- "top": 268
- },
- "post_job_actions": {
- "RenameDatasetActionoutput1": {
- "action_arguments": {
- "newname": "Filtered SNVMix output"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "output1"
- }
- },
- "tool_errors": null,
- "tool_id": "filter_snvmix",
- "tool_state": "{\"__page__\": 0, \"require_dual_strand\": \"\\\"yes\\\"\", \"input1\": \"null\", \"max_indels\": \"\\\"1\\\"\"}",
- "tool_version": "1.0.0",
- "type": "tool",
- "user_outputs": []
- },
- "6": {
- "annotation": "",
- "id": 6,
- "input_connections": {
- "codon_resource": {
- "id": 1,
- "output_name": "output"
- },
- "input1": {
- "id": 5,
- "output_name": "output1"
- },
- "known_snp_resource": {
- "id": 2,
- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "SNP filtering and pre-annotation",
- "outputs": [
- {
- "name": "output1",
- "type": "tabular"
- },
- {
- "name": "output2",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 539.5,
- "top": 467
- },
- "post_job_actions": {
- "RenameDatasetActionoutput2": {
- "action_arguments": {
- "newname": "codon-linked novel SNVs"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "output2"
- }
- },
- "tool_errors": null,
- "tool_id": "snp_filters",
- "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"known_snp_resource\": \"null\", \"codon_resource\": \"null\"}",
- "tool_version": "1.0.0",
- "type": "tool",
- "user_outputs": []
- },
- "7": {
- "annotation": "",
- "id": 7,
- "input_connections": {
- "input_codon": {
- "id": 6,
- "output_name": "output2"
- }
- },
- "inputs": [],
- "name": "SNV Annotator",
- "outputs": [
- {
- "name": "output_anno",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 891,
- "top": 223
- },
- "post_job_actions": {
- "RenameDatasetActionoutput_anno": {
- "action_arguments": {
- "newname": "Annotated novel SNVs from tumour"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "output_anno"
- }
- },
- "tool_errors": null,
- "tool_id": "snv_annotate",
- "tool_state": "{\"__page__\": 0, \"input_codon\": \"null\"}",
- "tool_version": "1.0.0",
- "type": "tool",
- "user_outputs": []
- },
- "8": {
- "annotation": "",
- "id": 8,
- "input_connections": {
- "input": {
- "id": 7,
- "output_name": "output_anno"
- }
- },
- "inputs": [],
- "name": "Select",
- "outputs": [
- {
- "name": "out_file1",
- "type": "input"
- }
- ],
- "position": {
- "left": 896,
- "top": 330
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "Grep1",
- "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"false\\\"\", \"pattern\": \"\\\"CODING\\\"\"}",
- "tool_version": "1.0.1",
- "type": "tool",
- "user_outputs": []
- },
- "9": {
- "annotation": "",
- "id": 9,
- "input_connections": {
- "input": {
- "id": 8,
- "output_name": "out_file1"
- }
- },
- "inputs": [],
- "name": "Cut",
- "outputs": [
- {
- "name": "out_file1",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 899,
- "top": 420
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "Cut1",
- "tool_state": "{\"columnList\": \"\\\"c1\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"Sp\\\"\", \"__page__\": 0}",
- "tool_version": "1.0.1",
- "type": "tool",
- "user_outputs": []
- },
- "10": {
- "annotation": "",
- "id": 10,
- "input_connections": {
- "input": {
- "id": 9,
- "output_name": "out_file1"
- }
- },
- "inputs": [],
- "name": "Convert",
- "outputs": [
- {
- "name": "out_file1",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 903,
- "top": 513
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "Convert characters1",
- "tool_state": "{\"input\": \"null\", \"convert_from\": \"\\\"Co\\\"\", \"__page__\": 0}",
- "tool_version": "1.0.0",
- "type": "tool",
- "user_outputs": []
- },
- "11": {
- "annotation": "",
- "id": 11,
- "input_connections": {
- "input1": {
- "id": 10,
- "output_name": "out_file1"
- }
- },
- "inputs": [],
- "name": "Trim",
- "outputs": [
- {
- "name": "out_file1",
- "type": "input"
- }
- ],
- "position": {
- "left": 904,
- "top": 607
- },
- "post_job_actions": {
- "RenameDatasetActionout_file1": {
- "action_arguments": {
- "newname": ""
- },
- "action_type": "RenameDatasetAction",
- "output_name": "out_file1"
- }
- },
- "tool_errors": null,
- "tool_id": "trimmer",
- "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"end\": \"\\\"0\\\"\", \"fastq\": \"\\\"\\\"\", \"ignore\": \"null\", \"start\": \"\\\"4\\\"\", \"col\": \"\\\"0\\\"\"}",
- "tool_version": "0.0.1",
- "type": "tool",
- "user_outputs": []
- },
- "12": {
- "annotation": "",
- "id": 12,
- "input_connections": {
- "pos": {
- "id": 11,
- "output_name": "out_file1"
- },
- "refOrHistory|input1": {
- "id": 3,
- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "SNVMix at selected positions",
- "outputs": [
- {
- "name": "output_snvmix",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 847.5,
- "top": 711
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "snvmix2",
- "tool_state": "{\"q\": \"\\\"19\\\"\", \"full\": \"\\\"yes\\\"\", \"__page__\": 0, \"refOrHistory\": \"{\\\"input1\\\": null, \\\"reference\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"keep_dups\": \"\\\"no\\\"\", \"pos\": \"null\", \"Q\": \"\\\"19\\\"\", \"keep_chastity\": \"\\\"no\\\"\", \"type\": \"\\\"MB\\\"\"}",
- "tool_version": "0.12.1-rc1",
- "type": "tool",
- "user_outputs": []
- },
- "13": {
- "annotation": "",
- "id": 13,
- "input_connections": {
- "input1": {
- "id": 12,
- "output_name": "output_snvmix"
- },
- "input2": {
- "id": 7,
- "output_name": "output_anno"
- }
- },
- "inputs": [],
- "name": "Get somatic positions from germline SNVMix output",
- "outputs": [
- {
- "name": "output1",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 1129,
- "top": 474.5
- },
- "post_job_actions": {
- "RenameDatasetActionoutput1": {
- "action_arguments": {
- "newname": "Final somatic calls (SNVMix1)"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "output1"
- }
- },
- "tool_errors": null,
- "tool_id": "snvmix_somatic_filter",
- "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"nonref_support\": \"\\\"2\\\"\", \"input1\": \"null\", \"posterior\": \"\\\"0.999\\\"\"}",
- "tool_version": "0.12.1-rc1",
- "type": "tool",
- "user_outputs": []
- }
- }
-}
\ No newline at end of file
diff -r a4975ec34575 -r 361d6506850a SNV/README
--- a/SNV/README Mon Oct 17 14:57:09 2011 -0400
+++ b/SNV/README Tue Oct 18 18:32:07 2011 -0400
@@ -3,8 +3,11 @@
Installation
------------
-1) Place these files in $GALAXY_HOME/tools
-2) Modify your configuration files appropriately, for example, add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section)
+1) Place these files in $GALAXY_HOME/tools and compile/install SNVMix2 if you haven't already done so (also copy/link the SNVMix2 binary,
+identify_nonsynonymous_mutations.pl and filter_snvmix.pl to /usr/local/bin or some other location in the default PATH, also ensure they are executable)
+2) Modify your configuration files appropriately
+-add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section), see the tool_conf.xml.sample for an example
+-create or modify $GALAXY_HOME/sam_fa_indices.loc to match the example provided (points galaxy to the fasta files containing the genome that was used during the alignment step). These are needed by SNVMix.
Requirements
------------
diff -r a4975ec34575 -r 361d6506850a SNV/filter_snvmix_somatic.py
--- a/SNV/filter_snvmix_somatic.py Mon Oct 17 14:57:09 2011 -0400
+++ b/SNV/filter_snvmix_somatic.py Tue Oct 18 18:32:07 2011 -0400
@@ -17,7 +17,7 @@
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.cookbook import doc_optparse
import re
-
+os.environ['LC_COLLATE'] = 'C'
def stop_err( msg ):
sys.stderr.write( '%s\n' % msg )
sys.exit()
diff -r a4975ec34575 -r 361d6506850a SNV/snp_filters.py
--- a/SNV/snp_filters.py Mon Oct 17 14:57:09 2011 -0400
+++ b/SNV/snp_filters.py Tue Oct 18 18:32:07 2011 -0400
@@ -19,6 +19,7 @@
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.cookbook import doc_optparse
+os.environ['LC_COLLATE'] = 'C'
def stop_err( msg ):
sys.stderr.write( '%s\n' % msg )
diff -r a4975ec34575 -r 361d6506850a SNV/tool-data/tool_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/tool-data/tool_conf.xml.sample Tue Oct 18 18:32:07 2011 -0400
@@ -0,0 +1,11 @@
+#add the following section to your file to enable these tools
+
+
diff -r a4975ec34575 -r 361d6506850a sam_fa_indices.loc.sample
--- a/sam_fa_indices.loc.sample Mon Oct 17 14:57:09 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files. You will need
-#to create these data files and then create a sam_fa_indices.loc file
-#similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The sam_fa_indices.loc
-#file has this format (white space characters are TAB characters):
-#
-#index
-#
-#So, for example, if you had hg18 indexed stored in
-#/depot/data2/galaxy/sam/,
-#then the sam_fa_indices.loc entry would look like this:
-#
-#index hg18 /depot/data2/galaxy/sam/hg18.fa
-#
-#and your /depot/data2/galaxy/sam/ directory
-#would contain hg18.fa and hg18.fa.fai files:
-#
-#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
-#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
-#
-#Your sam_fa_indices.loc file should include an entry per line for
-#each index set you have stored. The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file. For example:
-#
-#index hg18 /depot/data2/galaxy/sam/hg18.fa
-#index hg19 /depot/data2/galaxy/sam/hg19.fa
diff -r a4975ec34575 -r 361d6506850a tool_conf.xml.sample
--- a/tool_conf.xml.sample Mon Oct 17 14:57:09 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#add the following section to your file to enable these tools
-
-