GotCloud: Genetic Reference and Resource Files - Revision history

Mktrost: /* DBSNP VCF File */

2015-05-14T16:00:27Z

DBSNP VCF File

← Older revision		Revision as of 12:00, 14 May 2015
Line 82:		Line 82:
	! Configuration Key !! Default Value		! Configuration Key !! Default Value
	\|-		\|-
	\| DBSNP_VCF \|\| $(REF_DIR)/~~dbsnp_135~~.b37.vcf.gz		\| DBSNP_VCF \|\| $(REF_DIR)/dbsnp_142.b37.vcf.gz
	\|}		\|}
	{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"		{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"

Mktrost: /* Downloadable Reference and Resource Files */

2015-02-26T18:18:36Z

Downloadable Reference and Resource Files

← Older revision		Revision as of 14:18, 26 February 2015
Line 166:		Line 166:

	<ul>		<ul>
	<li> Human reference 37, dbsnp 135:</li>		<li> <div id="h37-db135">Human reference 37, dbsnp 135:</div></li>
	<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz</b>		<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz</b>
	<b>tar xzf h37-db135-v3.tgz</b>		<b>tar xzf h37-db135-v3.tgz</b>
	<b>rm -f h37-db135-v3.tgz</b>		<b>rm -f h37-db135-v3.tgz</b>
	<li>Human reference 37, dbsnp 142:</li>		<li><div id="h37-db142">Human reference 37, dbsnp 142:</div></li>
	<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db142-v1.tgz</b>		<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db142-v1.tgz</b>
	<b>tar xzf h37-db142-v1.tgz</b>		<b>tar xzf h37-db142-v1.tgz</b>
	<b>rm -f h37-db142-v1.tgz</b>		<b>rm -f h37-db142-v1.tgz</b>
	<li>Human reference 37 with decoy, dbsnp 142:</li>		<li><div id="hs37d5-db142">Human reference 37 with decoy, dbsnp 142:</div></li>
	<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/hs37d5-db142-v1.tgz</b>		<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/hs37d5-db142-v1.tgz</b>
	<b>tar xzf hs37d5-db142-v1.tgz</b>		<b>tar xzf hs37d5-db142-v1.tgz</b>
	<b>rm -f hs37d5-db142-v1.tgz</b>		<b>rm -f hs37d5-db142-v1.tgz</b>
	</ul>		</ul>

Mktrost: /* Downloadable Reference and Resource Files */

2015-02-24T15:53:05Z

Downloadable Reference and Resource Files

← Older revision		Revision as of 11:53, 24 February 2015
Line 174:		Line 174:
	<b>tar xzf h37-db142-v1.tgz</b>		<b>tar xzf h37-db142-v1.tgz</b>
	<b>rm -f h37-db142-v1.tgz</b>		<b>rm -f h37-db142-v1.tgz</b>
			<li>Human reference 37 with decoy, dbsnp 142:</li>
			<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/hs37d5-db142-v1.tgz</b>
			<b>tar xzf hs37d5-db142-v1.tgz</b>
			<b>rm -f hs37d5-db142-v1.tgz</b>
	</ul>		</ul>

Mktrost: /* Downloadable Reference and Resource Files */

2015-01-13T18:42:34Z

Downloadable Reference and Resource Files

← Older revision		Revision as of 14:42, 13 January 2015
Line 160:		Line 160:


	'''Get the Resource Files'''		'''Get & Install the Resource Files'''

	GotCloud makes use of various reference and other genetic resource files.		GotCloud makes use of various reference and other genetic resource files.
	You are free to use your own files, of course, but we also are making the files we use available.		You are free to use your own files, of course, but we also are making the files we use available.

	<~~code~~>		<ul>
			<li> Human reference 37, dbsnp 135:</li>
	<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz</b>		<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz</b>
	~~</code>~~


	~~'''Install the Resource Files'''~~

	~~<code>~~
	<b>tar xzf h37-db135-v3.tgz</b>		<b>tar xzf h37-db135-v3.tgz</b>
	<b>rm -f h37-db135-v3.tgz</b>		<b>rm -f h37-db135-v3.tgz</b>
	</~~code~~>		<li>Human reference 37, dbsnp 142:</li>
			<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db142-v1.tgz</b>
			<b>tar xzf h37-db142-v1.tgz</b>
			<b>rm -f h37-db142-v1.tgz</b>
			</ul>

Mktrost: /* Genetic Reference and Resource Files */

2015-01-05T18:40:07Z

Genetic Reference and Resource Files

← Older revision		Revision as of 14:40, 5 January 2015
Line 26:		Line 26:
	\| snpcall \|\| Must be tabixed		\| snpcall \|\| Must be tabixed
	\|-		\|-
	\| rowspan="2"\|[[#INDEL VCF File(s)\|INDEL VCF File(s)]] \|\| INDEL_PREFIX \|\| $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19 \|\| rowspan="2"\|snpcall \|\| ~~rowspan="2"\|Must~~ be ~~tabixed~~		\| rowspan="2"\|[[#INDEL VCF File(s)\|INDEL VCF File(s)]] \|\| INDEL_PREFIX \|\| $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19 \|\| rowspan="2"\|snpcall \|\| .chr#.vcf extension will be appended
	\|-		\|-
	\| INDEL_VCF \|\| ''alternate configuration setting if all INDEL sites are in a single VCF rather than broken up by chromosome''		\| INDEL_VCF \|\| ''alternate configuration setting if all INDEL sites are in a single VCF rather than broken up by chromosome''\|\|Must be tabixed
	\|}		\|}

Line 126:		Line 126:
	=== INDEL VCF File(s) ===		=== INDEL VCF File(s) ===
	VCF file containing known INDEL positions		VCF file containing known INDEL positions
	* Must be bgzip'd and tabix'd

	{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"		{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"

Mktrost: /* Downloadable Reference and Resource Files */

2014-12-02T15:09:27Z

Downloadable Reference and Resource Files

← Older revision		Revision as of 11:09, 2 December 2014
Line 154:		Line 154:
	<code>		<code>
	<b>cd gotcloud</b> # path to where you installed gotcloud		<b>cd gotcloud</b> # path to where you installed gotcloud
	~~<b>mkdir -p gotcloud.ref</b>~~
	~~<b>cd gotcloud.ref</b>~~
	</code>		</code>

Mktrost: /* Downloadable Reference and Resource Files */

2014-10-23T20:47:56Z

Downloadable Reference and Resource Files

← Older revision		Revision as of 16:47, 23 October 2014
Line 145:		Line 145:

	== Downloadable Reference and Resource Files ==		== Downloadable Reference and Resource Files ==
	*When running on Amazon, a default set of reference files are included in the GotCloud AMI.		* When running on Amazon, a default set of reference files are included in the GotCloud AMI in the default <code>REF_DIR</code>

Mktrost: /* Downloadable Reference and Resource Files */

2014-10-23T20:47:30Z

Downloadable Reference and Resource Files

← Older revision		Revision as of 16:47, 23 October 2014
Line 145:		Line 145:

	== Downloadable Reference and Resource Files ==		== Downloadable Reference and Resource Files ==
			*When running on Amazon, a default set of reference files are included in the GotCloud AMI.


	'''Installing Genetic Reference and Resource Files'''		'''Installing Genetic Reference and Resource Files'''

	Choose a destination for these files and install them as shown below. We'll assume you will use '''gotcloud/gotcloud.ref'''. Replace <code>gotcloud</code> with the path to where you installed gotcloud.		Choose a destination for these files and install them as shown below. We'll assume you will use '''gotcloud/gotcloud.ref'''. Replace <code>gotcloud</code> with the path to where you installed gotcloud.

Line 158:		Line 161:
	* <code>REF_DIR</code> in your configuration file		* <code>REF_DIR</code> in your configuration file
	* <code>--ref_dir</code> on the command-line		* <code>--ref_dir</code> on the command-line


	'''Get the Resource Files'''		'''Get the Resource Files'''
Line 166:		Line 170:
	<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz</b>		<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz</b>
	</code>		</code>


	'''Install the Resource Files'''		'''Install the Resource Files'''

Mktrost at 18:14, 23 October 2014

2014-10-23T18:14:50Z

← Older revision		Revision as of 14:14, 23 October 2014
Line 9:		Line 9:
	* To look in a different directory, set your reference/resource file location by setting either of the following to that path:		* To look in a different directory, set your reference/resource file location by setting either of the following to that path:
	** <code>REF_DIR</code> in your configuration file		** <code>REF_DIR</code> in your configuration file
	** <code>--~~refdir~~</code> on the command-line		** <code>--ref_dir</code> on the command-line

	{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"		{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
Line 157:		Line 157:
	If you use a path other than a gotcloud.ref subdirectory of gotcloud, note this path as you will need to set either of the following to the installation path:		If you use a path other than a gotcloud.ref subdirectory of gotcloud, note this path as you will need to set either of the following to the installation path:
	* <code>REF_DIR</code> in your configuration file		* <code>REF_DIR</code> in your configuration file
	* <code>--~~refdir~~</code> on the command-line		* <code>--ref_dir</code> on the command-line

	'''Get the Resource Files'''		'''Get the Resource Files'''

Mktrost: /* Downloadable Reference and Resource Files */

2014-10-23T18:13:05Z

Downloadable Reference and Resource Files

← Older revision		Revision as of 14:13, 23 October 2014
Line 155:		Line 155:
	</code>		</code>

	If you use a path other than a gotcloud.ref subdirectory of gotcloud, note this path as you will need to set the ~~variable '''~~REF_DIR~~'''~~ in ~~the~~ configuration file ~~to point to~~ the ~~installation path.~~		If you use a path other than a gotcloud.ref subdirectory of gotcloud, note this path as you will need to set either of the following to the installation path:
			* <code>REF_DIR</code> in your configuration file
			* <code>--refdir</code> on the command-line

	'''Get the Resource Files'''		'''Get the Resource Files'''