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)