Mercurial > repos > brasset_jensen > srnapipe
comparison README.md @ 58:e12ad81abcbb draft
Added quotes around fastq_n parameter.
| author | pierre.pouchin |
|---|---|
| date | Tue, 23 Oct 2018 10:36:18 -0400 |
| parents | 4bc00caa60b4 |
| children |
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| 57:fef39e626746 | 58:e12ad81abcbb |
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| 16 | 16 |
| 17 2. Some tools are used by sRNAPipe and must be installed and added to the Path. | 17 2. Some tools are used by sRNAPipe and must be installed and added to the Path. |
| 18 | 18 |
| 19 * Bwa aligner: you can obtain it here: https://sourceforge.net/projects/bio-bwa/files/ . Please download version 0.7.12-r1039 or higher | 19 * Bwa aligner: you can obtain it here: https://sourceforge.net/projects/bio-bwa/files/ . Please download version 0.7.12-r1039 or higher |
| 20 * 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. | 20 * 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. |
| 21 * Samtools : you can obtain it here : https://sourceforge.net/projects/samtools/files/samtools/1.2/. Please download version 1.2 | 21 * Samtools : you can obtain it here : https://sourceforge.net/projects/samtools/files/samtools/1.5/. Please download version 1.5 |
| 22 | 22 |
| 23 3. Perl version higher than 5.1 is needed with packages : "perl-statistics", "Parallel::ForkManager", "Statistics::R", "Getopt::Long" , "String::Random" installed. | 23 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. |
| 24 | 24 |
| 25 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 | 25 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 |
| 26 | 26 |
| 27 Installation | 27 Installation |
| 28 ============= | 28 ============= |