SPCM HPC Cluster Management
Lightweight Portable Job Scheduler
Another Programmer's Editor
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Auer Lab Github Site
Biostar-tools is a FreeBSD metaport that installs virtually all of the software referenced in the Biostar Handbook via one simple command:
pkg install biostar-tools
While FreeBSD users could utilize Miniconda as outlined in the handbook (see sysutils/linux-miniconda-installer), the biostar-tools metaport makes it easier to install and run the programs. There is no need to enable Linux compatibility, activate conda environments, etc. Simply install biostar-tools as described above, and all of the tools will be in the default PATH for everyone to use without jumping through any hoops.
Two of the software packages, ucsc-userapps and emboss, contain conflicts with other software and are therefore installed in special subdirectories. For example, bedGraphToBigWig is installed in /usr/local/userapps/bin instead of the normal /usr/local/bin and needle is installed in /usr/local/emboss/bin instead of the normal /usr/local/bin.
Rather than require users to alter their PATH by loading a module or activating a Conda environment, the FreeBSD ports for these tools add wrapper commands that are accessible via the normal path. Simply prefix the userapps or emboss commands with the wrapper as follows:
shell-prompt: kent bedGraphToBigWig [bedGraphToBigWig arguments] shell-prompt: emboss needle [needls arguments]