NgsCctsBuildVicuna - Revision history

Curtish@uab.edu: /* V_FAT */

2013-05-16T21:28:27Z

V_FAT

@@ Line 109: / Line 109: @@
    chmod +x *.pl
 * fix incorrectly spelled argument in vfat.pl
-  # inline patch
+ # inline patch
-  patch
+ patch < vfat.pl.mincontlen.patch

Curtish@uab.edu: /* V_FAT */

2013-05-16T21:23:14Z

V_FAT

← Older revision		Revision as of 21:23, 16 May 2013
Line 108:		Line 108:
	sed -i.orig '1 s\|^.perl\|#!'`which perl`'\|' .pl		sed -i.orig '1 s\|^.perl\|#!'`which perl`'\|' .pl
	chmod +x *.pl		chmod +x *.pl
			* fix incorrectly spelled argument in vfat.pl
			# inline patch
			patch
			*** vfat.pl 2013-05-16 16:18:45.344425015 -0500
			--- vfat.pl.bak 2013-05-16 16:19:36.077461441 -0500
			***************
			* 52,58 **

			GetOptions(
			"minlongcont=i" => \$option{minlongcont},
			! "mincontiglen=i" => \$option{mincontiglen},
			"readfa=s" => \$option{readfa},
			"readq=s" => \$option{readq},
			"readfa2=s" => \$option{readfa2},
			--- 52,58 ----

			GetOptions(
			"minlongcont=i" => \$option{minlongcont},
			! "mincontlen=i" => \$option{mincontlen},
			"readfa=s" => \$option{readfa},
			"readq=s" => \$option{readq},
			"readfa2=s" => \$option{readfa2},

Curtish@uab.edu: /* V_FAT */

2013-05-16T19:09:01Z

V_FAT

← Older revision		Revision as of 19:09, 16 May 2013
Line 101:		Line 101:
	cd /share/apps/ngs-ccts/VfatSoftwarePackage		cd /share/apps/ngs-ccts/VfatSoftwarePackage
	# first clean up perl path in configPaths.pl		# first clean up perl path in configPaths.pl
	sed -i.orig '1 s\|^.*perl\|#!~~/usr/bin/~~perl\|' configPaths.pl; diff configPaths.pl configPaths.pl.orig		sed -i.orig '1 s\|^.*perl\|#!'`which perl`'\|' configPaths.pl; diff configPaths.pl configPaths.pl.orig
	# then run it		# then run it
	./configPaths.pl ./configfile.txt		./configPaths.pl ./configfile.txt
			* clean up #! lines & perms - the configPaths.pl leaves an (illegal) space in there
			# set to /usr/bin/perl
			sed -i.orig '1 s\|^.perl\|#!'`which perl`'\|' .pl
			chmod +x *.pl

Curtish@uab.edu: /* V_FAT */

2013-05-16T18:57:38Z

V_FAT

← Older revision		Revision as of 18:57, 16 May 2013
Line 62:		Line 62:
	** export WISECONFIGDIR=/share/apps/ngs-ccts/wise2.2.0/wisecfg/		** export WISECONFIGDIR=/share/apps/ngs-ccts/wise2.2.0/wisecfg/
	** Caution: galaxy has GeneWise 1.0 - which may be in path!		** Caution: galaxy has GeneWise 1.0 - which may be in path!

			V_FAT
			* /share/apps/ngs-ccts/VfatSoftwarePackage
			* configfile.txt - backup
			mv configfile.txt configfile.txt.orig
			* configfile.txt - fill in paths
			# configfile.txt
			#
			# where VFAT is installed
			scriptpath = '/share/apps/ngs-ccts/VfatSoftwarePackage/'
			# ----------------------------------------------------------------
			# bin folder of the Mosaik distribution
			mosaikpath = '/share/apps/ngs-ccts/MOSAIK-2.1.73-source/bin/'
			# networkFile folder of your Mosaik distribution
			mosaiknetworkpath = '/share/apps/ngs-ccts/MOSAIK-2.1.73-source/networkFile/'
			# ----------------------------------------------------------------
			# samtools install path
			samtoolspath = '/share/apps/galaxy/galaxy-tools/bin/samtools/'
			# ----------------------------------------------------------------
			# Muscle 3.8 installation
			musclepath = '/share/apps/galaxy/galaxy-tools/bin/'
			# ----------------------------------------------------------------
			perlpath = '/usr/bin/perl'
			# ----------------------------------------------------------------
			# path for the binaries of your installation of wise2.2. It should
			# be in your wise2.2.0 folder under /src/bin/.
			genewisepath = '/share/apps/ngs-ccts/wise2.2.0/src/bin/'
			# path for config folder that is required by wise2.2. It
			# should be in your wise2.2.0 folder under /wisecfg/.
			genewisecfgpath = '/share/apps/ngs-ccts/wise2.2.0/wisecfg/'
			# ----------------------------------------------------------------
			# /share/apps/ngs-ccts/wise2.2.0/wisecfg
			Rpath = '/share/apps/galaxy/galaxy-tools/bin/'
			# ----------------------------------------------------------------
			# VICUNA/V-FAT species-specific reference data
			refDataPath = '/share/apps/ngs-ccts/VfatSoftwarePackage/ViralReferenceGenomes/'
			* run script to copy all scripts from configfile.txt into *.pl (ick!)
			cd /share/apps/ngs-ccts/VfatSoftwarePackage
			# first clean up perl path in configPaths.pl
			sed -i.orig '1 s\|^.*perl\|#!/usr/bin/perl\|' configPaths.pl; diff configPaths.pl configPaths.pl.orig
			# then run it
			./configPaths.pl ./configfile.txt

Curtish@uab.edu: /* Note: pre-built exe for Linux 64bit! */

2013-03-28T07:53:39Z

Note: pre-built exe for Linux 64bit!

← Older revision		Revision as of 07:53, 28 March 2013
Line 52:		Line 52:
	see [https://groups.google.com/forum/?hl=en&fromgroups=#!topic/viral-tool-users/kV8E3ll8TzM]		see [https://groups.google.com/forum/?hl=en&fromgroups=#!topic/viral-tool-users/kV8E3ll8TzM]
	but I've had some trouble with it. Now using only built version.		but I've had some trouble with it. Now using only built version.

			== V_FAT ==

			Pre-requisits
			* MUSCLE v3.8: /share/apps/galaxy/galaxy-tools/bin/muscle: MUSCLE v3.8.31
			* R 2.9+: /share/apps/galaxy/galaxy-tools/bin/R: R version 2.13.0 (2011-04-13)
			* Mosaik 2.1: /share/apps/ngs-ccts/MOSAIK_2.1.73-source/bin [[NgsCctsBuildMosaik]]
			* GeneWise 2.2.0: /share/apps/ngs-ccts/wise2.2.0: [[NgsCctsGeneWise]]
			** export WISECONFIGDIR=/share/apps/ngs-ccts/wise2.2.0/wisecfg/
			** Caution: galaxy has GeneWise 1.0 - which may be in path!

Curtish@uab.edu: /* Vicuna */

2013-03-28T07:39:42Z

Vicuna

← Older revision		Revision as of 07:39, 28 March 2013
Line 41:		Line 41:
	make		make

	build ~~analysis~~		build vicuna_analysis

	cd /share/apps/ngs-ccts/VICUNA_v1.2/scripts/vicuna_analysis		cd /share/apps/ngs-ccts/VICUNA_v1.2/scripts/vicuna_analysis

Curtish@uab.edu: /* Note: pre-built exe for Linux 64bit! */

2013-03-28T07:39:13Z

Note: pre-built exe for Linux 64bit!

← Older revision		Revision as of 07:39, 28 March 2013
Line 51:		Line 51:
	in the "executable" subdirectory!		in the "executable" subdirectory!
	see [https://groups.google.com/forum/?hl=en&fromgroups=#!topic/viral-tool-users/kV8E3ll8TzM]		see [https://groups.google.com/forum/?hl=en&fromgroups=#!topic/viral-tool-users/kV8E3ll8TzM]
			but I've had some trouble with it. Now using only built version.

Curtish@uab.edu: /* Vicuna */

2013-03-28T07:38:40Z

Vicuna

← Older revision		Revision as of 07:38, 28 March 2013
Line 31:		Line 31:
	unzip downloads/vicuna.v1.2.zip -x '__MACOSX/*'		unzip downloads/vicuna.v1.2.zip -x '__MACOSX/*'

	configure & build ~~- NOT NEEDED (see below)~~		configure & build

	cd /share/apps/ngs-ccts/VICUNA_v1.2/src		cd /share/apps/ngs-ccts/VICUNA_v1.2/src

Curtish@uab.edu: /* NCBI toolkit 7.0.0 */

2013-03-28T07:38:01Z

NCBI toolkit 7.0.0

← Older revision		Revision as of 07:38, 28 March 2013
Line 5:		Line 5:
	=== NCBI toolkit 7.0.0 ===		=== NCBI toolkit 7.0.0 ===

	'''~~WARNING~~''': ~~not needed - see [[NgsCctsBuildVicuna#Note:_pre-built_exe_for_Linux_64bit.21]] at bottom~~!		'''NOTE''': This takes a veyr long time!!!

	# download		# download

Curtish@uab.edu: /* Vicuna */

2013-01-09T12:02:46Z

Vicuna

← Older revision		Revision as of 12:02, 9 January 2013
Line 40:		Line 40:
	# !! Waiting for NCBI to finish building		# !! Waiting for NCBI to finish building
	make		make

			build analysis

			cd /share/apps/ngs-ccts/VICUNA_v1.2/scripts/vicuna_analysis
			make clean
			make all

	== Note: pre-built exe for Linux 64bit! ==		== Note: pre-built exe for Linux 64bit! ==