https://help.rc.ufl.edu/mediawiki/index.php?title=GDC-Client&feed=atom&action=history
GDC-Client - Revision history
2024-03-28T20:04:57Z
Revision history for this page on the wiki
MediaWiki 1.35.13
https://help.rc.ufl.edu/mediawiki/index.php?title=GDC-Client&diff=24818&oldid=prev
Israel.herrera at 18:57, 12 August 2022
2022-08-12T18:57:35Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:57, 12 August 2022</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
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<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Software]][[Category:Biology<del class="diffchange diffchange-inline">]][[Category:Bioinformatics</del>]][[Category:Sequencing]][[Category:NGS]]</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:NGS]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|<!--CONFIGURATION: REQUIRED--></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|<!--CONFIGURATION: REQUIRED--></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|{{#vardefine:app|gdc-client}}</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|{{#vardefine:app|gdc-client}}</div></td></tr>
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Israel.herrera
https://help.rc.ufl.edu/mediawiki/index.php?title=GDC-Client&diff=23827&oldid=prev
Israel.herrera at 17:21, 10 June 2022
2022-06-10T17:21:49Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:21, 10 June 2022</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l21" >Line 21:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!--Modules--></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!--Modules--></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>==<del class="diffchange diffchange-inline">Required </del>Modules==</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>==<ins class="diffchange diffchange-inline">Environment </ins>Modules==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Run <code>module spider </ins>{{#var:app}}<<ins class="diffchange diffchange-inline">/code</ins>> <ins class="diffchange diffchange-inline">to find out what environment modules are available for this application.</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">===Serial===</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* gcc/5.2.0</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* </del>{{#var:app}}</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><<del class="diffchange diffchange-inline">!--</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">===Parallel (OpenMP)===</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* intel</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* {{#var:app}}</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">===Parallel (MPI)===</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* intel</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* openmpi</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* {{#var:app}}</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">--</del>></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==System Variables==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==System Variables==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* HPC_{{uc:{{#var:app}}}}_DIR - installation directory</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* HPC_{{uc:{{#var:app}}}}_DIR - installation directory</div></td></tr>
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Israel.herrera
https://help.rc.ufl.edu/mediawiki/index.php?title=GDC-Client&diff=19014&oldid=prev
Moskalenko: Text replacement - "#uppercase" to "uc"
2019-12-06T21:21:08Z
<p>Text replacement - "#uppercase" to "uc"</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:21, 6 December 2019</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==System Variables==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==System Variables==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* HPC_{{<del class="diffchange diffchange-inline">#uppercase</del>:{{#var:app}}}}_DIR - installation directory</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* HPC_{{<ins class="diffchange diffchange-inline">uc</ins>:{{#var:app}}}}_DIR - installation directory</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!--Configuration--></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!--Configuration--></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{#if: {{#var: conf}}|==Configuration==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{#if: {{#var: conf}}|==Configuration==</div></td></tr>
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Moskalenko
https://help.rc.ufl.edu/mediawiki/index.php?title=GDC-Client&diff=14781&oldid=prev
Maxprok: Created page with "Category:SoftwareCategory:BiologyCategory:BioinformaticsCategory:SequencingCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|gdc-client}} |{{..."
2016-07-14T12:41:31Z
<p>Created page with "<a href="/doc/Category:Software" title="Category:Software">Category:Software</a><a href="/doc/Category:Biology" title="Category:Biology">Category:Biology</a><a href="/mediawiki/index.php?title=Category:Bioinformatics&action=edit&redlink=1" class="new" title="Category:Bioinformatics (page does not exist)">Category:Bioinformatics</a><a href="/doc/Category:Sequencing" title="Category:Sequencing">Category:Sequencing</a><a href="/doc/Category:NGS" title="Category:NGS">Category:NGS</a> {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|gdc-client}} |{{..."</p>
<p><b>New page</b></p><div>[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[Category:Sequencing]][[Category:NGS]]<br />
{|<!--CONFIGURATION: REQUIRED--><br />
|{{#vardefine:app|gdc-client}}<br />
|{{#vardefine:url|https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool}}<br />
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--><br />
|{{#vardefine:conf|}} <!--CONFIGURATION--><br />
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--><br />
|{{#vardefine:batch|}} <!--SLURM SCRIPTS--><br />
|{{#vardefine:policy|}} <!--POLICY--><br />
|{{#vardefine:testing|}} <!--PROFILING--><br />
|{{#vardefine:faq|}} <!--FAQ--><br />
|{{#vardefine:citation|}} <!--CITATION--><br />
|{{#vardefine:installation|}} <!--INSTALLATION--><br />
|}<br />
<!--BODY--><br />
<!--Description--><br />
{{#if: {{#var: url}}|<br />
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}<br />
<br />
The GDC provides a standard client-based mechanism in support of high performance data downloads and submission. The raw sequence files, typically stored as BAM or FASTQ, make up the bulk of data. The size for a single file can vary greatly depending on the specific analysis; However, some of the whole genome BAM files in The Cancer Genome Atlas (TCGA) reach sizes of 200-300 GB. In such cases, a high performance data download and submission client is essential.<br />
<br />
<!--Modules--><br />
==Required Modules==<br />
<br />
===Serial===<br />
* gcc/5.2.0<br />
* {{#var:app}}<br />
<!--<br />
===Parallel (OpenMP)===<br />
* intel<br />
* {{#var:app}}<br />
===Parallel (MPI)===<br />
* intel<br />
* openmpi<br />
* {{#var:app}}<br />
--><br />
==System Variables==<br />
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory<br />
<!--Configuration--><br />
{{#if: {{#var: conf}}|==Configuration==<br />
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.<br />
|}}<br />
<!--Run--><br />
{{#if: {{#var: exe}}|==Additional Information==<br />
<br />
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY<br />
<br />
|}}<br />
<!--SLURM scripts--><br />
{{#if: {{#var: batch}}|==Batch Script Examples==<br />
See the [[{{PAGENAME}}_batch]] page for {{#var: app}} batch script examples.<br />
|}}<br />
<!--Policy--><br />
{{#if: {{#var: policy}}|==Usage Policy==<br />
<br />
WRITE USAGE POLICY HERE (Licensing, usage, access).<br />
<br />
|}}<br />
<!--Performance--><br />
{{#if: {{#var: testing}}|==Performance==<br />
<br />
WRITE_PERFORMANCE_TESTING_RESULTS_HERE<br />
<br />
|}}<br />
<!--Faq--><br />
{{#if: {{#var: faq}}|==FAQ==<br />
*'''Q:''' **'''A:'''|}}<br />
<!--Citation--><br />
{{#if: {{#var: citation}}|==Citation==<br />
If you publish research that uses {{#var:app}} you have to cite it as follows:<br />
<br />
WRITE_CITATION_HERE<br />
<br />
|}}<br />
<!--Installation--><br />
{{#if: {{#var: installation}}|==Installation==<br />
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}<br />
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--><br />
__NOTOC____NOEDITSECTION__</div>
Maxprok