Provean 1.1.3 - Revision history

Prins0891: to

 to fix code blocks

2023-06-15T13:52:16Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 15:52, 15 June 2023
Line 5:		Line 5:
	/cm/shared/modulefiles/SHARED/		/cm/shared/modulefiles/SHARED/

	<~~source lang='tcl'~~>		<pre>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## Provean 1.1.3 modulefile		## Provean 1.1.3 modulefile
Line 21:		Line 21:


	</~~source~~>		</pre>

	== Installation details ==		== Installation details ==
	Compiled from source.		Compiled from source.
	<~~source lang='bash'~~>		<pre>
	./configure --prefix=/cm/shared/apps/SHARED/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/SHARED/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/lustre/shared/public_data_store/nrdb/nrdb_241213/nr		./configure --prefix=/cm/shared/apps/SHARED/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/SHARED/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/lustre/shared/public_data_store/nrdb/nrdb_241213/nr
	make		make
	make install		make install
	</~~source~~>		</pre>

	== See also ==		== See also ==

Megen002: /* Installation details */

2014-03-15T09:09:34Z

Installation details

← Older revision		Revision as of 11:09, 15 March 2014
Line 26:		Line 26:
	Compiled from source.		Compiled from source.
	<source lang='bash'>		<source lang='bash'>
	./configure --prefix=/cm/shared/apps/~~WUR/ABGC~~/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/~~WUR/ABGC~~/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/~~WUR/ABGC~~/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/~~WUR/ABGC~~/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/lustre~~/nobackup/WUR/ABGC~~/shared/public_data_store/nrdb/nrdb_241213/nr		./configure --prefix=/cm/shared/apps/SHARED/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/SHARED/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/lustre/shared/public_data_store/nrdb/nrdb_241213/nr
	make		make
	make install		make install

Megen002: /* Module file */

2014-03-15T09:03:04Z

Module file

← Older revision		Revision as of 11:03, 15 March 2014
Line 3:		Line 3:
	== Module file ==		== Module file ==
	The module file can be found in this location:		The module file can be found in this location:
	/cm/shared/~~apps~~/~~WUR~~/~~ABGC/modulefiles~~		/cm/shared/modulefiles/SHARED/

	<source lang='tcl'>		<source lang='tcl'>
Line 16:		Line 16:
	module-whatis "Adds Provean 1.1.3 to your environment"		module-whatis "Adds Provean 1.1.3 to your environment"

	set provean_113_root /cm/shared/apps/~~WUR/ABGC~~/provean/provean-1.1.3/bin/		set provean_113_root /cm/shared/apps/SHARED/provean/provean-1.1.3/bin/

	prepend-path PATH $provean_113_root		prepend-path PATH $provean_113_root
Line 22:		Line 22:

	</source>		</source>

	== Installation details ==		== Installation details ==
	Compiled from source.		Compiled from source.

Megen002: /* See also */

2013-12-27T10:51:57Z

Megen002: /* Installation details */

2013-12-24T22:06:07Z

Installation details

← Older revision		Revision as of 00:06, 25 December 2013
Line 25:		Line 25:
	Compiled from source.		Compiled from source.
	<source lang='bash'>		<source lang='bash'>
	./configure --prefix=/cm/shared/apps/WUR/ABGC/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/WUR/ABGC/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/cm/~~shared/apps~~/WUR/ABGC/~~public_data_resources~~/nrdb/nrdb_241213/nr		./configure --prefix=/cm/shared/apps/WUR/ABGC/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/WUR/ABGC/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/lustre/nobackup/WUR/ABGC/shared/public_data_store/nrdb/nrdb_241213/nr
	make		make
	make install		make install

Megen002: /* Installation details */

2013-12-24T20:23:46Z

Installation details

← Older revision		Revision as of 22:23, 24 December 2013
Line 23:		Line 23:
	</source>		</source>
	== Installation details ==		== Installation details ==
	Compiled from source ~~using~~.		Compiled from source.
	<source lang='bash'>		<source lang='bash'>
	./configure --prefix=/cm/shared/apps/WUR/ABGC/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/WUR/ABGC/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/cm/shared/apps/WUR/ABGC/public_data_resources/nrdb/nrdb_241213/nr		./configure --prefix=/cm/shared/apps/WUR/ABGC/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/WUR/ABGC/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/cm/shared/apps/WUR/ABGC/public_data_resources/nrdb/nrdb_241213/nr
Line 29:		Line 29:
	make install		make install
	</source>		</source>

	== See also ==		== See also ==
	* [[Globally_installed_software \| Globally installed software]]		* [[Globally_installed_software \| Globally installed software]]

Megen002: /* External links */

2013-12-24T20:23:29Z

External links

← Older revision		Revision as of 22:23, 24 December 2013
Line 34:		Line 34:

	== External links ==		== External links ==
	* [http://~~samtools~~.~~sourceforge~~.~~net Samtools page on Sourceforge~~]		* [http://provean.jcvi.org/downloads/provean.acmbcb.pdf Provean paper]
			* [http://provean.jcvi.org/about.php Explanation of Provean algorithm]]
			* [http://provean.jcvi.org/downloads/README Provean README]
			* [ftp://ftp.ncbi.nih.gov/blast/db/ Location of nr. db. at NCBI]
			* [http://weizhong-lab.ucsd.edu/cd-hit/ CD-HIT official website]

Megen002: Created page with "[http://provean.jcvi.org/about.php PROVEAN] was developed to predict whether a protein sequence variation affects protein function. == Module file == The module file can be f..."

2013-12-24T20:19:11Z

Created page with "[http://provean.jcvi.org/about.php PROVEAN] was developed to predict whether a protein sequence variation affects protein function. == Module file == The module file can be f..."

New page

[http://provean.jcvi.org/about.php PROVEAN] was developed to predict whether a protein sequence variation affects protein function.

== Module file ==
The module file can be found in this location:
/cm/shared/apps/WUR/ABGC/modulefiles

<source lang='tcl'>
#%Module1.0#######################################################################
## Provean 1.1.3 modulefile
##
proc ModulesHelp { } {

puts stderr "\tAdds Provean 1.1.3 to your environment"
}

module-whatis "Adds Provean 1.1.3 to your environment"

set provean_113_root /cm/shared/apps/WUR/ABGC/provean/provean-1.1.3/bin/

prepend-path PATH $provean_113_root

</source>
== Installation details ==
Compiled from source using.
<source lang='bash'>
./configure --prefix=/cm/shared/apps/WUR/ABGC/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/WUR/ABGC/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/cm/shared/apps/WUR/ABGC/public_data_resources/nrdb/nrdb_241213/nr
make
make install
</source>
== See also ==
* [[Globally_installed_software | Globally installed software]]
* [[ABGC_modules | ABGC specific modules]]

== External links ==
* [http://samtools.sourceforge.net Samtools page on Sourceforge]

← Older revision		Revision as of 12:51, 27 December 2013
Line 33:		Line 33:
	* [[Globally_installed_software \| Globally installed software]]		* [[Globally_installed_software \| Globally installed software]]
	* [[ABGC_modules \| ABGC specific modules]]		* [[ABGC_modules \| ABGC specific modules]]
			* [[Provean_Sus_scrofa \| Mapping all known Sus scrofa variants with Provean]]

	== External links ==		== External links ==