Mercurial > repos > matt-shirley > sra_tools
changeset 47:04cc8176e86f draft default tip
update to SRA toolkit 2.3.3-3
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 16 Sep 2013 20:27:28 -0400 |
| parents | 88a13a2fd23f |
| children | |
| files | fastq_dump.xml sam_dump.xml sra_pileup.xml tool_dependencies.xml |
| diffstat | 4 files changed, 16 insertions(+), 16 deletions(-) [+] |
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--- a/fastq_dump.xml Tue Sep 03 22:02:30 2013 -0400 +++ b/fastq_dump.xml Mon Sep 16 20:27:28 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="fastq_dump" name="Extract reads" version="1.1.0"> +<tool id="fastq_dump" name="Extract reads" version="1.1.1"> <description> from NCBI SRA.</description> <command> fastq-dump --log-level fatal @@ -112,7 +112,7 @@ <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/> </stdio> <requirements> - <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> + <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> </requirements> <help> This tool extracts reads from SRA archives using fastq-dump.
--- a/sam_dump.xml Tue Sep 03 22:02:30 2013 -0400 +++ b/sam_dump.xml Mon Sep 16 20:27:28 2013 -0400 @@ -88,7 +88,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> + <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> </requirements> <help> This tool extracts reads from sra archives using sam-dump.
--- a/sra_pileup.xml Tue Sep 03 22:02:30 2013 -0400 +++ b/sra_pileup.xml Mon Sep 16 20:27:28 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="sra_pileup" name="Generate pileup format" version="1.0.1"> +<tool id="sra_pileup" name="Generate pileup format" version="1.1.1"> <description> from NCBI sra.</description> <command>sra-pileup --log-level fatal #if str( $region ) != "": @@ -40,7 +40,7 @@ <data format="pileup" name="output"/> </outputs> <requirements> - <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> + <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> </requirements> <help> This tool produces pileup format from sra archives using sra-pileup.
--- a/tool_dependencies.xml Tue Sep 03 22:02:30 2013 -0400 +++ b/tool_dependencies.xml Mon Sep 16 20:27:28 2013 -0400 @@ -1,18 +1,18 @@ <?xml version="1.0"?> <tool_dependency> - <package name="sra_toolkit" version="2.3.2-4"> + <package name="sra_toolkit" version="2.3.3-3"> <install version="1.0"> <actions> - <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.2-4/sra_sdk-2.3.2-4.tar.gz</action> - <action type="shell_command">make release</action> - <action type="shell_command">make static</action> - <action type="shell_command">make</action> - <action type="make_directory">$INSTALL_DIR/bin</action> - <action type="make_directory">$INSTALL_DIR/ncbi</action> - <action type="make_directory">$INSTALL_DIR/ncbi/public</action> - <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action> - <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> - <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> + <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sra_sdk-2.3.3-3.tar.gz</action> + <action type="shell_command">make release</action> + <action type="shell_command">make static</action> + <action type="shell_command">make</action> + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="make_directory">$INSTALL_DIR/ncbi</action> + <action type="make_directory">$INSTALL_DIR/ncbi/public</action> + <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action> + <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> + <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> </actions> </install> <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.