[ARVADOS] updated: f4d92dbb53d31a3577f0b52a7b54c92762090cdc

[git at public.curoverse.com]

Summary of changes:
 crunch_scripts/arvados-bcbio-nextgen.py | 67 ++++++++-------------------------
 1 file changed, 15 insertions(+), 52 deletions(-)

       via  f4d92dbb53d31a3577f0b52a7b54c92762090cdc (commit)
      from  ec0278bcf9affbbe9f88c413116f6aaa2713e0f6 (commit)

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commit f4d92dbb53d31a3577f0b52a7b54c92762090cdc
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 2 16:41:57 2014 -0400

    tool-data in work

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index 5281737..ea2e7b4 100755
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -11,50 +11,13 @@ if len(arvados.current_task()['parameters']) > 0:
 else:
     p = arvados.current_job()['script_parameters']
 
-t = arvados.current_task().tmpdir
-
 os.unlink("/usr/local/share/bcbio-nextgen/galaxy")
 os.mkdir("/usr/local/share/bcbio-nextgen/galaxy")
 shutil.copy("/usr/local/share/bcbio-nextgen/config/bcbio_system.yaml", "/usr/local/share/bcbio-nextgen/galaxy")
 
-os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/tool-data")
-
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/tool_data_table_conf.xml", "w") as f:
-    f.write('''<tables>
-    <!-- Locations of indexes in the BWA mapper format -->
-    <table name="bwa_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie2 mapper format -->
-    <table name="bowtie2_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie2_indices.loc" />
-    </table>
-    <!-- Locations of indexes in the Bowtie2 mapper format for TopHat2 to use -->
-    <table name="tophat2_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie2_indices.loc" />
-    </table>
-    <!-- Location of SAMTools indexes and other files -->
-    <table name="sam_fa_indexes" comment_char="#">
-        <columns>index, value, path</columns>
-        <file path="tool-data/sam_fa_indices.loc" />
-    </table>
-    <!-- Location of Picard dict file and other files -->
-    <table name="picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Location of Picard dict files valid for GATK -->
-    <table name="gatk_picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/gatk_sorted_picard_index.loc" />
-    </table>
-</tables>
-''')
+os.chdir(arvados.current_task().tmpdir)
 
-with open("/tmp/crunch-job/gatk-variant.yaml", "w") as f:
+with open("gatk-variant.yaml", "w") as f:
     f.write('''
 # Template for whole genome Illumina variant calling with GATK pipeline
 ---
@@ -77,27 +40,27 @@ details:
       # variant_regions: /path/to/your.bed
 ''')
 
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bowtie2_indices.loc", "w") as f:
+rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "gatk-variant.yaml", "project1",
+                         subst.do_substitution(p, "$(file $(R1))"),
+                         subst.do_substitution(p, "$(file $(R2))")])
+
+os.chdir("project1/work")
+
+os.mkdir("tool-data")
+
+with open("tool-data/bowtie2_indices.loc", "w") as f:
     f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(dir $(bowtie2_indices))"))
 
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bwa_indices.loc", "w") as f:
+with open("tool-data/bwa_indices.loc", "w") as f:
     f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(bwa_indices))"))
 
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/gatk_sorted_picard_index.loc", "w") as f:
+with open("tool-data/gatk_sorted_picard_index.loc", "w") as f:
     f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(gatk_sorted_picard_index))"))
 
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/picard_index.loc", "w") as f:
+with open("tool-data/picard_index.loc", "w") as f:
     f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(picard_index))"))
 
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc", "w") as f:
+with open("tool-data/sam_fa_indices.loc", "w") as f:
     f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))"))
 
-os.chdir(arvados.current_task().tmpdir)
-
-rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/gatk-variant.yaml", "project1",
-                         subst.do_substitution(p, "$(file $(R1))"),
-                         subst.do_substitution(p, "$(file $(R2))")])
-
-os.chdir("project1/work")
-
 rcode = subprocess.call(["bcbio_nextgen.py", "../config/project1.yaml"])

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