| Previous changeset 24:22d9fe442c50 (2015-03-30) Next changeset 26:7d80b2b24270 (2015-03-30) |
|
Commit message:
Update tool requirement versions. |
|
modified:
fastq_dump.xml sam_dump.xml sra_pileup.xml tool_dependencies.xml |
| b |
| diff -r 22d9fe442c50 -r 393a04ec0fa9 fastq_dump.xml --- a/fastq_dump.xml Mon Mar 30 21:33:57 2015 -0400 +++ b/fastq_dump.xml Mon Mar 30 21:57:40 2015 -0400 |
| b |
| @@ -112,7 +112,7 @@ <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/> </stdio> <requirements> - <requirement type="package" version="2.3.4-2">sra_toolkit</requirement> + <requirement type="package" version="2.4.5">sra_toolkit</requirement> </requirements> <help> This tool extracts reads from SRA archives using fastq-dump. |
| b |
| diff -r 22d9fe442c50 -r 393a04ec0fa9 sam_dump.xml --- a/sam_dump.xml Mon Mar 30 21:33:57 2015 -0400 +++ b/sam_dump.xml Mon Mar 30 21:57:40 2015 -0400 |
| b |
| @@ -88,7 +88,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="2.3.4-2">sra_toolkit</requirement> + <requirement type="package" version="2.4.5">sra_toolkit</requirement> </requirements> <help> This tool extracts reads from sra archives using sam-dump. |
| b |
| diff -r 22d9fe442c50 -r 393a04ec0fa9 sra_pileup.xml --- a/sra_pileup.xml Mon Mar 30 21:33:57 2015 -0400 +++ b/sra_pileup.xml Mon Mar 30 21:57:40 2015 -0400 |
| b |
| @@ -1,6 +1,6 @@ <tool id="sra_pileup" name="Generate pileup format" version="1.1.1"> <description> from NCBI sra.</description> - <command>sra-pileup --log-level fatal + <command>sra-pileup --log-level fatal #if str( $region ) != "": --aligned-region $region #end if @@ -10,7 +10,7 @@ #if $input.input_select == "file": $input.file #elif $input.input_select == "accession_number": - $input.accession + $input.accession #elif $input.input_select == "text": `cat $input.text` #end if @@ -40,11 +40,11 @@ <data format="pileup" name="output"/> </outputs> <requirements> - <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> + <requirement type="package" version="2.4.5">sra_toolkit</requirement> </requirements> <help> - This tool produces pileup format from sra archives using sra-pileup. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + This tool produces pileup format from sra archives using sra-pileup. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help> |
| b |
| diff -r 22d9fe442c50 -r 393a04ec0fa9 tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 30 21:33:57 2015 -0400 +++ b/tool_dependencies.xml Mon Mar 30 21:57:40 2015 -0400 |
| b |
| @@ -26,7 +26,9 @@ cd $INSTALL_DIR/bin ./vdb-config -s "cache-enabled = false" </action> - <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> </actions> </install> <readme> |