diff README.txt @ 7:eda59b985b1c draft default tip

Uploaded

--- a/README.txt	Tue Jun 28 02:59:32 2016 -0400
+++ b/README.txt	Mon Mar 13 08:21:19 2017 -0400
@@ -1,86 +1,87 @@
-==============================
-          MutSpec-Suite        
-==============================
-
-Created by Maude Ardin and Vincent Cahais (Mechanisms of Carcinogenesis Section, International Agency for Research on Cancer F69372 Lyon France,
-http://www.iarc.fr/)
-
-Version 1.0
-
-Released under GNU public license version 2 (GPL v2)
-
-Package description: Ardin et al. - 2016 - MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse
-cancer genomes - BMC Bioinformatics
-http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z
-
-Test data: https://usegalaxy.org/u/maude-ardin/p/mutspectestdata
-
-
-
-### Requirements
-
-	# python-dev
-build-essential and python-dev packages must be installed on your machine before installing MutSpec tools:
-$ sudo apt-get install build-essential python-dev
-
-
-	# Annovar
-If you do not have ANNOVAR installed, you can download it here: http://www.openbioinformatics.org/annovar/annovar_download_form.php
-
-1) Once downloaded, install annovar per the installation instructions and edit the PATH variable in galaxy deamon (/etc/init.d/galaxy)
-to reflect the location of directory containing perl scripts.
-
-2) Create directories for saving Annovar databases
-	2-a Create a folder (annovardb) for saving all Annovar databases, e.g. hg19db
-	2-b Create a subfolder (seqFolder) for saving the reference genome, e.g. hg19db/hg19_seq
-
-3) Download the reference genome (by chromosome) from UCSC for all desired builds as follows:
-$ annotate_variation.pl -buildver <build> -downdb seq <seqFolder>
-
-where <build> can be hg18, hg19 or hg38 for the human genome or mm9, mm10 for the mouse genome.
-and <seqFolder> is the location where the sequences (by chromosme) should be stored, e.g. hg19db/hg19_seq
-
-
-4) Download all desired databases for all desired builds as follows:
-$ annotate_variation.pl -buildver <build> [-webfrom annovar] -downdb <database> <annovardb>
-
-/!\ At least the database refGene must be downloaded /!\
-
-where <build> can be hg18, hg19 or hg38 for the human genome or mm9, mm10 for the mouse genome.
-and <database> is the database file to download, e.g. refGene
-and <annovardb> is the location where all database files should be stored, e.g. hg19db
-
-The list of all available databases can be found here: http://annovar.openbioinformatics.org/en/latest/user-guide/download/
-
-
-5) Edit the annovar_index.loc file (in the folder galaxy-dist/tool-data/toolshed/repos/iarc/mutspec/revision/) to reflect the location
-of annovardb folder (containing all the databases files downloaded from Annovar).
-Restart galaxy instance for changes in .loc file to take effect or reload it into the admin interface.
-
-6) Edit the file build_listAVDB.txt in the mutspec install directory to reflect the name and the type of the databases installed
-
-
-### Installation
-
-	# MutSpec-Stat and MutSpec-NMF
-By default 8 CPUs are used by these tools, but you may edit mutspecStat_wrapper.sh and mutspecNmf_wrapper.sh to change this number
-to the maximum number of CPU available on your server.
-
-MutSpec-Stat and MutSpec-NMF tools allow parallel computations that are time consuming.
-It is recommended to use the highest number of cores available on the Galaxy server to reduce the computation time of these tools.
-
-
-
-
-	# MutSpec-Annot
-The maximum CPU value needs to be specified when installing MutSpec package by editing the file mutspecAnnot.pl to reflect the maximum number
-of CPU available on your server.
-
-This tool may be time consuming for large files. For example, annotating a file of more than 25,000 variants takes 1 hour using 1 CPU (2.6 GHz),
-while annotating this file using 8 CPUs takes only 5 minutes.
-We have optimized MutSpec-Annot so that the tool uses more CPUs, if available, as follows:
--files with less than 5,000 lines: 1 CPU is used
--files with more than 5,000 and less than 25,000 lines: 2 CPUs are used
--files with more than 25,000 and less than 100,000 lines: 8 (or maximum CPUs, if less than 8 CPUs are available) are used (our benchmark
-results didn't show any time saving using more than 8 cores for files with more than 25,000 but less than 100,000 lines)
--files with more than 100,000: maximum CPUs are used 
+======================================================================
+          MutSpec-Suite: Readme file for Galaxy installation        
+======================================================================
+
+Created by Maude Ardin and Vincent Cahais (Mechanisms of Carcinogenesis Section, International Agency for Research on Cancer F69372 Lyon France,
+http://www.iarc.fr/)
+
+Version 1.0
+
+Released under GNU public license version 2 (GPL v2)
+
+Package description: Ardin et al. - 2016 - MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse
+cancer genomes - BMC Bioinformatics
+http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z
+
+Test data: https://usegalaxy.org/u/maude-ardin/p/mutspectestdata
+
+Source code: https://github.com/IARCbioinfo/mutspec
+
+
+### Requirements
+
+	# python-dev
+build-essential and python-dev packages must be installed on your machine before installing MutSpec tools:
+$ sudo apt-get install build-essential python-dev
+
+
+	# Annovar
+If you do not have ANNOVAR installed, you can download it here: http://www.openbioinformatics.org/annovar/annovar_download_form.php
+
+1) Once downloaded, install annovar per the installation instructions and edit the PATH variable in galaxy deamon (/etc/init.d/galaxy)
+to reflect the location of directory containing perl scripts.
+
+2) Create directories for saving Annovar databases
+	2-a Create a folder (annovardb) for saving all Annovar databases, e.g. hg19db
+	2-b Create a subfolder (seqFolder) for saving the reference genome, e.g. hg19db/hg19_seq
+
+3) Download the reference genome (by chromosome) from UCSC for all desired builds as follows:
+$ annotate_variation.pl -buildver <build> -downdb seq <seqFolder>
+
+where <build> can be hg18, hg19 or hg38 for the human genome or mm9, mm10 for the mouse genome.
+and <seqFolder> is the location where the sequences (by chromosme) should be stored, e.g. hg19db/hg19_seq
+
+
+4) Download all desired databases for all desired builds as follows:
+$ annotate_variation.pl -buildver <build> [-webfrom annovar] -downdb <database> <annovardb>
+
+/!\ At least the database refGene must be downloaded /!\
+
+where <build> can be hg18, hg19 or hg38 for the human genome or mm9, mm10 for the mouse genome.
+and <database> is the database file to download, e.g. refGene
+and <annovardb> is the location where all database files should be stored, e.g. hg19db
+
+The list of all available databases can be found here: http://annovar.openbioinformatics.org/en/latest/user-guide/download/
+
+
+5) Edit the annovar_index.loc file (in the folder galaxy-dist/tool-data/toolshed/repos/iarc/mutspec/revision/) to reflect the location
+of annovardb folder (containing all the databases files downloaded from Annovar).
+Restart galaxy instance for changes in .loc file to take effect or reload it into the admin interface.
+
+6) Edit the file build_listAVDB.txt in the mutspec install directory to reflect the name and the type of the databases installed
+
+
+### Installation
+
+	# MutSpec-Stat and MutSpec-NMF
+By default 8 CPUs are used by these tools, but you may edit mutspecStat_wrapper.sh and mutspecNmf.xml to change this number
+to the maximum number of CPU available on your server.
+
+MutSpec-Stat and MutSpec-NMF tools allow parallel computations that are time consuming.
+It is recommended to use the highest number of cores available on the Galaxy server to reduce the computation time of these tools.
+
+
+
+
+	# MutSpec-Annot
+The maximum CPU value needs to be specified when installing MutSpec package by editing the file mutspecAnnot.pl to reflect the maximum number
+of CPU available on your server.
+
+This tool may be time consuming for large files. For example, annotating a file of more than 25,000 variants takes 1 hour using 1 CPU (2.6 GHz),
+while annotating this file using 8 CPUs takes only 5 minutes.
+We have optimized MutSpec-Annot so that the tool uses more CPUs, if available, as follows:
+-files with less than 5,000 lines: 1 CPU is used
+-files with more than 5,000 and less than 25,000 lines: 2 CPUs are used
+-files with more than 25,000 and less than 100,000 lines: 8 (or maximum CPUs, if less than 8 CPUs are available) are used (our benchmark
+results didn't show any time saving using more than 8 cores for files with more than 25,000 but less than 100,000 lines)
+-files with more than 100,000: maximum CPUs are used