Difference between revisions of "SRA"
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|{{#vardefine:app|sra}} | |{{#vardefine:app|sra}} | ||
|{{#vardefine:url|http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software}} | |{{#vardefine:url|http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software}} | ||
| − | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> |
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
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into a single script, configuration-assistant.perl that helps users download the correct references | into a single script, configuration-assistant.perl that helps users download the correct references | ||
for a given cSRA file and configure the user environment for the SRA Toolkit. | for a given cSRA file and configure the user environment for the SRA Toolkit. | ||
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<!--Modules--> | <!--Modules--> | ||
==Required Modules== | ==Required Modules== | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
* HPC_SRA_BIN - location of the executables directory | * HPC_SRA_BIN - location of the executables directory | ||
* HPC_SRA_DOC - location of the documentation directory | * HPC_SRA_DOC - location of the documentation directory | ||
| − | + | <!--Additional--> | |
| − | ==Aspera Connect== | + | {{#if: {{#var: exe}}|==Additional Information== |
| + | ===Aspera Connect=== | ||
To download SRA data you can use the "ascp" utility from the [http://asperasoft.com/downloads/ Aspera Connect] browser plugin package. We have a copy installed and provided by the sra module. A wrapper script ''ascp.sh'' that automatically uses the ssh key is available. For instance: | To download SRA data you can use the "ascp" utility from the [http://asperasoft.com/downloads/ Aspera Connect] browser plugin package. We have a copy installed and provided by the sra module. A wrapper script ''ascp.sh'' that automatically uses the ssh key is available. For instance: | ||
| − | |||
ascp.sh -QT anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz faa | ascp.sh -QT anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz faa | ||
| − | |||
will download the all.faa.tar.gz archive to the faa directory. | will download the all.faa.tar.gz archive to the faa directory. | ||
'''Note:''' if the download fails to start on the first try with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" | '''Note:''' if the download fails to start on the first try with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" | ||
error just re-run the command. It's a DNS (host name resolution) problem, which will resolve itself. | error just re-run the command. It's a DNS (host name resolution) problem, which will resolve itself. | ||
| − | + | |}} | |
| − | |||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
Revision as of 19:55, 10 August 2012
Description
This is the NCBI Short Read Archive Toolkit.
Release notes:
SRA Toolkit 2.1.7a includes new features in sam-dump tool and vdb-dump tools.
Sam-dump now supports slicing across multiple sequences, and dumping cSRA files to fasta and fastq formats. In addition, sam-dump has three new parameters:
-=|--hide-identical Output '=' if base is identical to reference --gzip Compress output using gzip --bzip2 Compress output using bzip2
vdb-dump has two new parameters
-o|--column_enum_short enumerates columns in short form -b|--boolean defines how boolean's are printed (1,T)
We have combined the functionality of two scripts, config-assistant.perl and reference-assistant.perl into a single script, configuration-assistant.perl that helps users download the correct references for a given cSRA file and configure the user environment for the SRA Toolkit.
Required Modules
Serial
- sra
System Variables
- HPC_{{#uppercase:sra}}_DIR - installation directory
- HPC_SRA_BIN - location of the executables directory
- HPC_SRA_DOC - location of the documentation directory
Additional Information
Aspera Connect
To download SRA data you can use the "ascp" utility from the Aspera Connect browser plugin package. We have a copy installed and provided by the sra module. A wrapper script ascp.sh that automatically uses the ssh key is available. For instance:
ascp.sh -QT anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz faa
will download the all.faa.tar.gz archive to the faa directory.
Note: if the download fails to start on the first try with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" error just re-run the command. It's a DNS (host name resolution) problem, which will resolve itself.