Difference between revisions of "SRA"
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Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
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__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#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|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | ||
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|{{#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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This is the NCBI Short Read Archive Toolkit. | This is the NCBI Short Read Archive Toolkit. | ||
| − | + | ;Note: sra will create a $HOME/ncib/public directory and cache the prefetched data files there. However, home directory has a 20gb limit and its use for job data storage is a violation of the [https://www.rc.ufl.edu/about/policies/storage/ UFRC storage policy]. You must change that location to a directory in your ufrc space before running the sra toolkit. The official approach is to use the vdb-config tool | |
| + | vdb-config -i | ||
| + | and change the directory to, for example, /blue/$GROUP/$USER/ncbi/public. See the [https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration SRA Toolkit Configuration Documentation] for more details. | ||
| − | + | Alternatively, create an 'ncbi' directory in your /blue space and symlink it to ~/ncbi. E.g. | |
| − | + | $ mkdir /blue/mygroup/$USER/ncbi | |
| − | + | $ ln -s /blue/mygroup/$USER/ncbi ~/ncbi | |
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| − | + | ==Uploads== | |
| − | + | It appears that data uploads to NCBI only work from login servers. Start a screen session before beginning an upload if there are any concerns about being disconnected. | |
| − | + | <!--Modules--> | |
| − | + | ==Environment Modules== | |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | + | ==System Variables== | |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |
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| − | <!-- | ||
| − | == | ||
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| − | {{ | ||
* 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: | ||
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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 | ||
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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 | + | '''Note:''' if the download fails to run with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" |
| − | error | + | error please submit a support request. This means that the remote site has not been allowed through the firewall. Please be sure to include the path to a script you used to run the data transfer command into the request. Do not put any sensitive information like passwords, keys, and such into the request. |
| − | + | |}} | |
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{{#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.|}} | ||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Revision as of 15:56, 22 August 2022
Description
This is the NCBI Short Read Archive Toolkit.
- Note
- sra will create a $HOME/ncib/public directory and cache the prefetched data files there. However, home directory has a 20gb limit and its use for job data storage is a violation of the UFRC storage policy. You must change that location to a directory in your ufrc space before running the sra toolkit. The official approach is to use the vdb-config tool
vdb-config -i
and change the directory to, for example, /blue/$GROUP/$USER/ncbi/public. See the SRA Toolkit Configuration Documentation for more details.
Alternatively, create an 'ncbi' directory in your /blue space and symlink it to ~/ncbi. E.g.
$ mkdir /blue/mygroup/$USER/ncbi $ ln -s /blue/mygroup/$USER/ncbi ~/ncbi
Uploads
It appears that data uploads to NCBI only work from login servers. Start a screen session before beginning an upload if there are any concerns about being disconnected.
Environment Modules
Run module spider sra to find out what environment modules are available for this application.
System Variables
- HPC_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 run with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" error please submit a support request. This means that the remote site has not been allowed through the firewall. Please be sure to include the path to a script you used to run the data transfer command into the request. Do not put any sensitive information like passwords, keys, and such into the request.