| Previous changeset 57:fef39e626746 (2018-09-13) Next changeset 59:eeb89c3331ad (2018-10-23) |
|
Commit message:
Added quotes around fastq_n parameter. |
|
modified:
README.md sRNAPipe.xml |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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": |