Recent changes to Running EricScript

WikiPage Running EricScript modified by matteo.benelli

matteo.benelli — Tue, 22 Nov 2011 09:42:48 -0000

--- v6 
+++ v7 
@@ -1,14 +1,26 @@
-After you download EricScript, copy the program folder to your preferred location.
-The first time you run EricScript, you need to make ericscript.pl executable and to create the indexes required by BWA to perform the alignment.
-
-chmod +x /PATH/TO/ERIC/ericscript.pl
-bwa index -a bwtsw /PATH/TO/ERIC/lib/Ref.fa/EnsemblGene.Reference.fa 
-
-To obtain more information on how running EricScript, digit:
-
-/PATH/TO/ERIC/ericscript.pl
-
-To run EricScript with default parameters, simply digit:
-
-/PATH/TO/ERIC/ericscript.pl -name samplename -o /PATH/TO/OUTPUT/ reads_1.fastq(.gz) reads_2.fastq(.gz)
+Once you have downloaded EricScript, extract the package
+
+> tar -xjf ericscript.tar.bz2
+
+Make a copy of the program folder to your favorite location.
+Before running for the first time EricScript, you need to make ericscript.pl executable:
+
+> chmod +x /PATH/TO/ERIC/ericscript.pl
+
+Then, you need to download the pre-built Ensembl Database:
+
+> /PATH/TO/ERIC/ericscript.pl --checkdb
+
+To get information about running EricScript, digit:
+
+> /PATH/TO/ERIC/ericscript.pl --help
+
+To run a demonstration of EricScript pipeline on a synthetic dataset, digit:
+
+> /PATH/TO/ERIC/ericscript.pl --demo
+
+To run EricScript with default parameters, digit:
+
+> /PATH/TO/ERIC/ericscript.pl -name SAMPLENAME -o /PATH/TO/OUTPUT/YOUR_FASTQ_1  /PATH/TO/OUTPUT/YOUR_FASTQ_2
+

WikiPage Running EricScript modified by matteo.benelli

matteo.benelli — Tue, 11 Oct 2011 14:09:58 -0000

--- v5 
+++ v6 
@@ -4,6 +4,10 @@
 chmod +x /PATH/TO/ERIC/ericscript.pl
 bwa index -a bwtsw /PATH/TO/ERIC/lib/Ref.fa/EnsemblGene.Reference.fa 
 
+To obtain more information on how running EricScript, digit:
+
+/PATH/TO/ERIC/ericscript.pl
+
 To run EricScript with default parameters, simply digit:
 
 /PATH/TO/ERIC/ericscript.pl -name samplename -o /PATH/TO/OUTPUT/ reads_1.fastq(.gz) reads_2.fastq(.gz)

WikiPage Running EricScript modified by matteo.benelli

matteo.benelli — Tue, 11 Oct 2011 14:05:31 -0000

--- v4 
+++ v5 
@@ -1,5 +1,5 @@
 After you download EricScript, copy the program folder to your preferred location.
-The first time you run EricScript, you need to make ericscript.pl executable and to index database sequences in the FASTA format by using BWA.
+The first time you run EricScript, you need to make ericscript.pl executable and to create the indexes required by BWA to perform the alignment.
 
 chmod +x /PATH/TO/ERIC/ericscript.pl
 bwa index -a bwtsw /PATH/TO/ERIC/lib/Ref.fa/EnsemblGene.Reference.fa

WikiPage Running EricScript modified by matteo.benelli

matteo.benelli — Tue, 11 Oct 2011 14:04:27 -0000

--- v3 
+++ v4 
@@ -1,7 +1,7 @@
 After you download EricScript, copy the program folder to your preferred location.
 The first time you run EricScript, you need to make ericscript.pl executable and to index database sequences in the FASTA format by using BWA.
 
-chamod +x /PATH/TO/ERIC/ericscript.pl
+chmod +x /PATH/TO/ERIC/ericscript.pl
 bwa index -a bwtsw /PATH/TO/ERIC/lib/Ref.fa/EnsemblGene.Reference.fa 
 
 To run EricScript with default parameters, simply digit:

WikiPage Running EricScript modified by matteo.benelli

matteo.benelli — Tue, 11 Oct 2011 14:04:14 -0000

--- v2 
+++ v3 
@@ -1,10 +1,10 @@
 After you download EricScript, copy the program folder to your preferred location.
 The first time you run EricScript, you need to make ericscript.pl executable and to index database sequences in the FASTA format by using BWA.
 
-chamod +x */path/to/ericscript/*ericscript.pl
-bwa index -a bwtsw */path/to/ericscript*/lib/Ref.fa/EnsemblGene.Reference.fa 
-
+chamod +x /PATH/TO/ERIC/ericscript.pl
+bwa index -a bwtsw /PATH/TO/ERIC/lib/Ref.fa/EnsemblGene.Reference.fa 
+
 To run EricScript with default parameters, simply digit:
 
-*/path/to/ericscript/*ericscript.pl -name samplename -o */path/to/output/* your_reads_1.fastq(.gz) your_reads_2.fastq(.gz)
+/PATH/TO/ERIC/ericscript.pl -name samplename -o /PATH/TO/OUTPUT/ reads_1.fastq(.gz) reads_2.fastq(.gz)

WikiPage Running EricScript modified by matteo.benelli

matteo.benelli — Tue, 11 Oct 2011 14:02:30 -0000

--- v1 
+++ v2 
@@ -1,10 +1,10 @@
 After you download EricScript, copy the program folder to your preferred location.
 The first time you run EricScript, you need to make ericscript.pl executable and to index database sequences in the FASTA format by using BWA.
 
-chamod +x */path/to/ericscript*/ericscript.pl
+chamod +x */path/to/ericscript/*ericscript.pl
 bwa index -a bwtsw */path/to/ericscript*/lib/Ref.fa/EnsemblGene.Reference.fa 
 
 To run EricScript with default parameters, simply digit:
 
-*/path/to/ericscript*ericscript.pl -name samplename -o */path/to/output/* your_reads_1.fastq(.gz) your_reads_2.fastq(.gz)
+*/path/to/ericscript/*ericscript.pl -name samplename -o */path/to/output/* your_reads_1.fastq(.gz) your_reads_2.fastq(.gz)

WikiPage Running EricScript modified by matteo.benelli

matteo.benelli — Tue, 11 Oct 2011 14:00:54 -0000

After you download EricScript, copy the program folder to your preferred location. The first time you run EricScript, you need to make ericscript.pl executable and to index database sequences in the FASTA format by using BWA. chamod +x */path/to/ericscript*/ericscript.pl bwa index -a bwtsw */path/to/ericscript*/lib/Ref.fa/EnsemblGene.Reference.fa To run EricScript with default parameters, simply digit: */path/to/ericscript*ericscript.pl -name samplename -o */path/to/output/* your_reads_1.fastq(.gz) your_reads_2.fastq(.gz)