News:New biostar-tools metaport for FreeBSD

Question

[bacon4000]

FYI, FreeBSD users can now install all the bioinformatics software referenced by the Biostar Handbook via FreeBSD ports. Everything except bedGraphToBigWig can be installed simply by running

pkg install biostar-tools

bedGraphToBigWig is part of ucsc-userapps, which cannot be redistributed for licensing reasons, so there is no binary package. However, the FreeBSD ports system allows installing from source as easily as from a binary package (though it will take much longer), so restrictive licenses are not a major hurdle. ucsc-userapps can be easily installed separately by running

cd /usr/ports/biology/ucsc-userapps && make install

This will prompt you to accept the license terms and then automatically download from UCSC, build, and install.

Note that these installations are an alternative to conda/pip. If you have installed via FreeBSD ports/packages, you can skip all of the conda/pip commands in the handbook.

All programs are installed into the default PATH (/usr/local/bin) except for emboss and ucsc-userapps, which have multiple command-name conflicts with other programs. To use emboss commands, add /usr/local/emboss/bin to your PATH:

For Bourne-shell derivatives: (sh, bash, dash, zsh, ...)

export PATH=/usr/local/emboss/bin:$PATH

For C-shell derivatives: (csh, tcsh)

setenv PATH /usr/local/emboss/bin:$PATH

Or from any shell, you can run a separate shell process with the augmented PATH rather than hack the environment of your current shell:

env PATH=/usr/local/emboss/bin:$PATH bash

Replace "bash" with the shell of your choice. Then simply exit the shell to restore your previous PATH.

For UCSC-userapps, add /usr/local/bin/userapps.

The ports also install convenience scripts ucsc-shell and emboss-shell for quickly enabling the tools for interactive use. These scripts run a sub-shell with the proper directory prepended to PATH.

For anyone who is not a FreeBSD user but interested in trying it out, I would recommend GhostBSD for Unix novices. It's very much like Ubuntu Linux with a graphical installer and management tools.

For the more Unix-savvy, there is also the desktop-installer app, which adds virtually any desktop environment to a stock FreeBSD system:

http://acadix.biz/desktop-installer.php

Please report any problems with biostar-tools or other FreeBSD ports on the FreeBSD site:

https://www.freebsd.org/support/bugreports/

Questions posted on this forum may never be seen by the right people.

Cheers,

-Jason

Answer 1

[bacon4000]

Added these wrappers for emboss and ucsc-utils so that we don't have to load a module or alter PATH in any other way. So now we can run all the tools necessary for the handbook from a standard directory.

Maybe they'll be useful to others as well.

/***************************************************************************
 *  Description:
 *      Wrapper to turn emboss commands into subcommands.  The emboss suite
 *      contains executables that conflict with multiple other software
 *      packages and therefore cannot be safely installed directly under a
 *      standard prefix.  This wrapper can be installed under the standard
 *      PATH and used to to execute emboss commands installed under a
 *      private prefix, without altering PATH, activating a special
 *      environment, opening a container, etc.  This sub-command paradigm
 *      is already familiar to bioinformaticians thanks to other suites
 *      like samtools, bedtools, etc.
 *
 *      Example:
 *
 *          emboss seqret args
 *
 *      instead of one of the following:
 *
 *          prefix/bin/seqret args
 *
 *          env PATH=prefix/bin:$PATH seqret args
 *
 *          conda activate emboss
 *          seqret args
 *
 *  Arguments:
 *      The full emboss command you would use if it were in PATH.
 *
 *  Compile with EMBOSS_PREFIX set to the parent of the bin directory
 *  containing the emboss binaries.
 *
 *  History: 
 *  Date        Name        Modification
 *  2021-09-13  Jason Bacon Begin
 ***************************************************************************/

#include <stdio.h>
#include <sysexits.h>
#include <limits.h>
#include <unistd.h>

#ifndef EMBOSS_PREFIX
#define EMBOSS_PREFIX   "/usr/local/emboss"
#endif

int     main(int argc,char *argv[])

{
    char    cmd[PATH_MAX + 1];

    if ( argc < 2 )
    {
        fprintf(stderr, "Usage: %s emboss-command [args]\n", argv[0]);
        return EX_USAGE;
    }

    snprintf(cmd, PATH_MAX, "%s/bin/%s", EMBOSS_PREFIX, argv[1]);
    execv(cmd, argv + 1);
}

/***************************************************************************
 *  Description:
 *      Wrapper to turn ucsc kent commands into subcommands.  The kent suite
 *      contains executables that conflict with multiple other software
 *      packages and therefore cannot be safely installed directly under a
 *      standard prefix.  This wrapper can be installed under the standard
 *      PATH and used to to execute kent commands installed under a
 *      private prefix, without altering PATH, activating a special
 *      environment, opening a container, etc.  This sub-command paradigm
 *      is already familiar to bioinformaticians thanks to other suites
 *      like samtools, bedtools, etc.
 *
 *      Example:
 *
 *          kent bigWigToBedGraph args
 *
 *      instead of one of the following:
 *
 *          prefix/bin/bigWigToBedGraph args
 *
 *          env PATH=prefix/bin:$PATH bigWigToBedGraph args
 *
 *          conda activate kent
 *          bigWigToBedGraph args
 *
 *  Arguments:
 *      The full kent utils command you would use if it were in PATH.
 *
 *  Compile with UCSC_PREFIX set to the parent of the bin directory
 *  containing the kent binaries.
 *
 *  History: 
 *  Date        Name        Modification
 *  2021-09-13  Jason Bacon Begin
 ***************************************************************************/

#include <stdio.h>
#include <sysexits.h>
#include <limits.h>
#include <unistd.h>

#ifndef UCSC_PREFIX
#define UCSC_PREFIX   "/usr/local/userapps"
#endif

int     main(int argc,char *argv[])

{
    char    cmd[PATH_MAX + 1];

    if ( argc < 2 )
    {
        fprintf(stderr, "Usage: %s UCSC-userapps-command [args]\n", argv[0]);
        return EX_USAGE;
    }

    snprintf(cmd, PATH_MAX, "%s/bin/%s", UCSC_PREFIX, argv[1]);
    execv(cmd, argv + 1);
}