Package Types

Each tool/library package we maintain is a sub-directory under package_downloads root directory.

Package Categories

We have the following categories of packages --

1. The package has no git repos - we get the release version from static files -

   • Blat ( install done from binaries)
   • R (install running a set of commands)

2. The package has a git repos but the git repos does not tag new releases - we get the release version from static files-

   • Hisat2 ( install from source running a set of commands)
   • Trimmomatic ( install done from binaries)

3. The package has a git repos with release tags and the install is done from git export version tarball - then run the install commands.

   • Bamtools
   • Bedtools
   • Bowtie
   • Bowtie2
   • Bwa
   • Cutadapt
   • Htslib
   • Samtools
   • Star
   • Toil

4. The package has a git repos with release tags - But package version downloaded from site

   • Boost (install from source running a set of commands)
   • Fastx_toolkit (install from source running a set of commands)
   • Eigen (install done from binaries/libraries)
   • Cufflinks ( install done from binaries)
   • Fastqc ( install done from binaries)
   • Kallisto ( install done from binaries)
   • Picard ( install done from binaries)
   • Salmon ( install done from binaries)
   • Stringtie ( install done from binaries)
   • Tophat ( install done from binaries)
   • Trimgalore ( install done from binaries)

Tools We Install From Binaries

1. Blat
2. Cufflinks
3. Eigen Libraries
4. Fastqc
5. Jenkins
6. Kallisto
7. Picard
8. Salmon
9. Stringtie
10. Tophat
11. Trimgalore
12. Trimmomatic

Tools We Install From Source

1. Bamtools
2. Bedtools
3. Bwa
4. Bowtie
5. Bowtie2
6. Cutadapt
7. Fastx Toolkit
8. Hisat2
9. HtsLib
10. Jsoncpp
11. R-package
12. Sammtools
13. Star
14. Toil
15. RSEM