UMass Boston

Applications on local clusters are generally accessible via one of several options:

1. They are located on the default path.  This generally true for most software provided by the OS, such as editors, etc.
2. They are accessible via the module commands.
3. They are located within the shared software directory.  This directory is /share/apps.  On gibbs, software applications can be found in /shared/software.  Some packages may also be under /opt or /usr/local.
4. Software can also be installed local to a user account.  This may be the best option if you are the sole user of the application, or if it is regularly being modified and recompiled.

In general, using the system software or software via the module command is preferred (options 1 and 2, above).  Depending on your specific needs, it may be more appropriate to set the appropriate environment variables directly in your scripts or makefiles (i.e. option 3).   

Please email us for any additional applications you may need for your research at: it-rc@umb.edu.

Available applications chimera:

•   ANNOTATE: ANNOTATE/3.05
•   AnsysEM: AnsysEM/16.1
•   FastQC: FastQC/0.11.3
•   LAMMPS: LAMMPS/stable-9Dec14-mpich_g++, ...
•   PyMOL: PyMOL/1.7.6.6
•   R: R/3.1.2
•   SGA: SGA/0.10.13
•   SGE: SGE/8.1.8
•   StdEnv: StdEnv
•   abyss: abyss/1.9.0
•   acml/5.3.1: acml/5.3.1/gfortran64_fma4_mp, ...
•   bamtools: bamtools/2.3.0
•   bcftools: bcftools/2015.08.19
•   bcl2fastq: bcl2fastq/1.8.4, bcl2fastq/2.16.0.10
•   bedtools: bedtools/2.22
•   blast: blast/2.2.26, blast/2.2.30+
•   boost: boost/1.57.0
•   bowtie2: bowtie2/2.2.4
•   bwa: bwa/0.7.9a
•   cloog: cloog/0.18.1
•   discovarexp: discovarexp/52196
•   fastStructure: fastStructure/1.0
•   gaussian: gaussian/g09
•   gcc: gcc/4.4.7, gcc/4.9.2 GNU Compiler Family (C/C++/Fortran for x86_64) 
•   gmp: gmp/4.3.2
•   gsl: gsl/1.16
•   hdf5: hdf5/1.8.15
•   htslib: htslib/1.2.1
•   hydrolight: hydrolight/5.1.4
•   intel: intel/composer_xe_2013.1.117
•   isl: isl/0.12.2
•   jdk: jdk/1.7.0_75, jdk/1.8.0_31
•   lmod: lmod/5.8 Lmod: An Environment Module System
•   maq: maq/0.7.1
•   matlab: matlab/R2014b
•   matplotlib/python-2.7.9: matplotlib/python-2.7.9/1.4.3
•   matplotlib/python-3.4.2: matplotlib/python-3.4.2/1.4.3
•   misopy/python-2.7.9: misopy/python-2.7.9/0.5.3
•   misopy/python-3.4.2: misopy/python-3.4.2/0.5.3
•   modtran: modtran/5.3
•   mpc: mpc/1.0.1
•   mpfr: mpfr/3.1.2
•   mpich: mpich/3.1.3
•   numpy/python-2.7.9: numpy/python-2.7.9/1.9.2
•   numpy/python-3.4.2: numpy/python-3.4.2/1.9.2
•   open64: open64/5.0 open64 Compiler Family (C/C++/Fortran90/Fortran95 for x86_64) 
•   openmpi: openmpi/1.8.3, openmpi/1.10.0
•   pysam/python-2.7.9: pysam/python-2.7.9/0.8.2.1
•   pysam/python-3.4.2: pysam/python-3.4.2/0.8.2.1
•   python: python/2.7.9, python/3.4.2
•   qiime/python-2.7.9: qiime/python-2.7.9/1.9.1
•   samtools: samtools/1.2
•   scala: scala/2.10.4
•   schrodinger: schrodinger/2015-3
•   scipy/python-2.7.9: scipy/python-2.7.9/0.15.1
•   scipy/python-3.4.2: scipy/python-3.4.2/0.15.1
•   settarg: settarg/5.8
•   sortmerna: sortmerna/2.0
•   spark: spark/1.5.2
•   splicemap: splicemap/3.3.5.2
•   sratoolkit: sratoolkit/2.4.5-2
•   stochpy/python-2.7.9: stochpy/python-2.7.9/2.2
•   stochpy/python-3.4.2: stochpy/python-3.4.2/2.2
•   structure: structure/2.3.4
•   sumaclust: sumaclust/1.0
•   swarm: swarm/1.2.19
•   tophat: tophat/2.0.13
•   usearch: usearch/6.1