# HG changeset patch
# User pierre.pouchin
# Date 1540305378 14400
# Node ID e12ad81abcbba594040c898a6dd9b740c84b69f2
# Parent  fef39e626746c57fd69ba119b7e557110a91d9c1
Added quotes around fastq_n parameter.

diff -r fef39e626746 -r e12ad81abcbb README.md
--- a/README.md	Thu Sep 13 11:45:05 2018 -0400
+++ b/README.md	Tue Oct 23 10:36:18 2018 -0400
@@ -18,9 +18,9 @@
 
 	* Bwa aligner: you can obtain it here: https://sourceforge.net/projects/bio-bwa/files/ . Please download version  0.7.12-r1039 or higher
 	* BedTools powerful toolset for genome arithmetic is also needed. It should be found here: http://bedtools.readthedocs.io/en/latest/ . We recommend to use v2.24.0 or higher.
-	* Samtools : you can obtain it here :  https://sourceforge.net/projects/samtools/files/samtools/1.2/. Please download version 1.2
+	* Samtools : you can obtain it here :  https://sourceforge.net/projects/samtools/files/samtools/1.5/. Please download version 1.5
 
-3. Perl version higher than 5.1 is needed with packages : "perl-statistics", "Parallel::ForkManager", "Statistics::R", "Getopt::Long" , "String::Random" installed.
+3. Perl version higher than 5.1 is needed with packages : "perl-statistics", "Parallel::ForkManager", "Statistics::R", "Getopt::Long" , "String::Random", "File::Copy::Recursive" and "Math::CDF" installed.
 
 4. R project version higher than 3.1 is needed with libraries "plotrix", "bioconductor-sushi", "RColorBrewer" and "ggplot2"  installed. You can find respectively these libraries here: https://cran.r-project.org/web/packages/plotrix/index.html and https://bioconductor.org/packages/release/bioc/html/Sushi.html and https://cran.r-project.org/web/packages/RColorBrewer/index.html and https://cran.r-project.org/web/packages/ggplot2/index.html
 
diff -r fef39e626746 -r e12ad81abcbb sRNAPipe.xml
--- a/sRNAPipe.xml	Thu Sep 13 11:45:05 2018 -0400
+++ b/sRNAPipe.xml	Tue Oct 23 10:36:18 2018 -0400
@@ -5,10 +5,10 @@
     ./bin/sRNAPipe.pl
 
     --fastq ${first_input}
-    --fastq_n ${first_input.name}
+    --fastq_n "${first_input.name}"
     #for $input_file in $input_files:
     --fastq ${input_file.additional_input}
-    --fastq_n ${input_file.additional_input.name}
+    --fastq_n "${input_file.additional_input.name}"
     #end for
 
     #if $Genome.refGenomeSource == "history":