Biostar-Tools is a metaport for installing all the tools necessary to
work through the Biostar Handbook.
The handbook instructs the reader to install these tools mostly via
bioconda, which then requires the user to activate the bioconda
environment each time they want to use the tools. You can also
install conda packages on FreeBSD if you wish. For details, see
/usr/ports/sysutils/linux-miniconda-installer/pkg-descr
Biostar-tools installs all of the tools except emboss to the
default PATH (normally /usr/local/bin) so they just work without any
special environment. Emboss commands are installed to
/usr/local/emboss/bin due to conflicts with other packages. Run
"biostar-shell" to add the emboss commands to your PATH, and simply
exit the shell to return your PATH to normal.
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above )
biology/biostar-tools: Allow package build on non-amd64 systems
Only sra-tools is still non-portable, but it will take some time to
add support for other architectures. In the meantime, allow aarch64
and powerpc64 users to have a biostar-tools package.
biostar-tools: Add new deps to metaport
csvkit, miller: Tools for working with comma-separated data
py-ont-fast5-api: Library and tools for Oxford Nanopore fast5 files
biology/biostar-tools: Meta-port for Biostar Handbook tools
Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions. If you need bedGraphToBigWig, run
cd /usr/ports/biology/ucsc-userapps && make install clean
