Refactoring this package

[LucyHut]

For each package - get rid of code redundancies by refactoring the following:

1. Config files
2. Install scripts
3. Download scripts

Notes: We have the following types of packages --

1. The package has no git repos - version check using release notes -

   • 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 - version check using release notes -

   • 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)

[LucyHut]

Done:

1. Created a main script getToolVersion.sh that will be scheduled to check for
   new releases - before, this was done by each tool

2. Combined the two main install scripts - runDownloadGitRepos.sh and
   runDownloadPackage.sh - into one runPackageInstall.sh

3. deleted getCurrentReleaseNumber.sh

4. Added a new script gitExportRepos.sh to export git repos

5. Added a new wrapper script install_package.sh that calls the tool's Install script

6. Added few new script - check_package_install.sh

7. Standardized the name of the tool's configuration file to : toolName_package.cfg

8. Refactored each tool's config file

9. Refactored and tested the Install script of the following 3 tools: R, blat, hisat2

10. Tested getToolVersion.sh for all the tools

11. Added new global variable BINARIES_INSTALL to package config where we install from binaries

12. Added new global variables to package dependencies file where we install from binaries
    BIN_FILES=
    BIN_DIR=""
    INCLUDE_DIR=""
    LIB64_DIR=""
    LIB_DIR=""

13. Create a new script install_binaries.sh to run the install of package that have BINARIES_INSTALL=true

14. Added a new script setToolVersion.sh to manually set the tool's version to download

[LucyHut]

To Do

1. Refactor and test the Install script of the remaining tools
2. Documentation
3. Review/update the dependencies file of each tool
4. Download the package and test the tools install on linux servers other than biocore servers

[jhgraber]

I think I know what you mean, but just to be sure, can you define for me your use of the term "refactoring"

[LucyHut]

Code Refactoring: The process of cleaning the code without changing its functionality

See :https://refactoring.guru/refactoring
[](Code Refactoring)