| Prossima revisione | Revisione precedente |
| calcoloscientifico:softwareapplicativonew1:lifesci [29/11/2018 11:31] – creata fausto.pagani | calcoloscientifico:softwareapplicativonew1:lifesci [22/02/2019 11:12] (versione attuale) – fabio.spataro |
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| ^ Name ^ Version ^ Installation ^ Module ^ note ^ | ^ Name ^ Version ^ Installation ^ Module ^ note ^ |
| ^ APPLICATIONS / TOOLS ^^^^^ | ^ APPLICATIONS/TOOLS ^^^^^ |
| | [[.:priv:cluster:softwareapplicativo:Crystal14 ]] | 1.04 | /hpc/share | crystal14/1.0.4 (todo) | | | [[..:priv:cluster:softwareapplicativo:Crystal14]] | 1.04 | /hpc/share | crystal14/1.0.4 (todo) | |
| | Matlab | R2011a | /hpc/share | matlab/R2011a | | | [[..:priv:cluster:softwareapplicativo:R]] | 3.3.3 | module | gnu R_base/3.3.2 | https://www.r-project.org | |
| | Matlab | R2017a | /hpc/share | matlab/R2017a (default) | | | [[..:priv:cluster:softwareapplicativo:Gromacs]] | 4.5.7, 5.1.4 | /hpc/share | no | http://www.gromacs.org | |
| | FSDA | | /hpc/share | toolkit di matlab/R2017a | http://www.riani.it/MATLAB/FSDA/index.html| | | [[..:priv:cluster:softwareapplicativo:Amber]] | 11 | /hpc/share | | http://ambermd.org | |
| | Octave | 3.8.2 | rpm | no | https://www.gnu.org/software/octave/ | | | [[..:priv:cluster:softwareapplicativo:AutoDock]] | 4.2.6 | /hpc/share | | | |
| | [[.:priv:cluster:softwareapplicativo:R]] | 3.3.3 | module | gnu R_base/3.3.2 | https://www.r-project.org/ | | | [[..:priv:cluster:softwareapplicativo:Samtools]] | 1.6 | /hpc/share | | http://www.htslib.org | |
| | [[.:priv:cluster:softwareapplicativo:QE]] | 5.4.0 | rpm | no | http://www.quantum-espresso.org/ | | | [[..:priv:cluster:softwareapplicativo:Star]] | 2.5.3a | /hpc/share | | https://github.com/alexdobin/STAR | |
| | [[.:priv:cluster:softwareapplicativo:Gromacs ]] | 4.5.7, 5.1.4 | /hpc/share | no | http://www.gromacs.org/ | | | [[..:priv:cluster:softwareapplicativo:Bedtools]] | 2.25.0 | /hpc/share | | http://bedtools.readthedocs.io/en/latest | |
| | [[.:priv:cluster:softwareapplicativo:Gaussian ]] | 09, 16 | /hpc/share | | http://gaussian.com/ | | | [[..:priv:cluster:softwareapplicativo:Bowtie]] | 1.2.2 | /hpc/share | | http://bowtie-bio.sourceforge.net/index.shtml | |
| | [[.:priv:cluster:softwareapplicativo:Amber ]] | 11 | /hpc/share | | http://ambermd.org/ | | | [[..:priv:cluster:softwareapplicativo:Bowtie2]] | 2.3.3.1 | /hpc/share | | http://bowtie-bio..sourceforge.net/bowtie2/index.shtml | |
| | [[.:priv:cluster:softwareapplicativo:Schrodinger ]] | 2017 | /hpc/share | | | | | [[..:priv:cluster:softwareapplicativo:espresso md]] | | /hpc/share | virtualenv/espresso | http://espressomd.org/wordpress | |
| | [[.:priv:cluster:softwareapplicativo:Abaqus ]] | 2017, 2018 | /hpc/share | | https://en.wikipedia.org/wiki/Abaqus | | | [[..:priv:cluster:softwareapplicativo:namd]] | | /hpc/share | | http://www.ks.uiuc.edu/Research/namd | |
| | [[.:priv:cluster:softwareapplicativo:Emboss ]] | 6.6.0 | /hpc/share | | http://emboss.sourgeforge.net | | | [[..:priv:cluster:softwareapplicativo:mpi4py]] | | rpm ohpc | | https://mpi4py.readthedocs.io/en/stable | |
| | [[.:priv:cluster:softwareapplicativo:Itpp ]] | 4.4.1 | /hpc/share | | http://itpp.sourceforge.net | | | [[..:priv:cluster:softwareapplicativo:SPAdes]] | 3.13.0 | /hpc/share | modulefiles/spades | http://cab.spbu.ru/software/spades | |
| | [[.:priv:cluster:softwareapplicativo:AutoDock ]] | 4.2.6 | /hpc/share | | | | [[..:priv:cluster:softwareapplicativo:Unicycler]] | 0.4.7 | /hpc/share | virtualenv/unicycler | https://github.com/rrwick/Unicycler | |
| | [[.:priv:cluster:softwareapplicativo:fds ]] | 6.5.3 | /hpc/share | | https://github.com/firemodels/fds/wiki | | | [[..:priv:cluster:softwareapplicativo:Prokka]] | 1.13.4 | /hpc/share | modulefiles/prokka | https://github.com/tseemann/prokka | |
| | [[.:priv:cluster:softwareapplicativo:sentaurus ]] | 2017.09 | /hpc/share | sentaurus| | | | [[..:priv:cluster:softwareapplicativo:ABySS]] | 2.1.15 | /hpc/share | moduledeps/gnu-openmpi/abyss | http://www.bcgsc.ca/platform/bioinfo/software/abyss | |
| | [[.:priv:cluster:softwareapplicativo: Samtools]] | 1.6 | /hpc/share | |http://www.htslib.org/ | | | [[..:priv:cluster:softwareapplicativo:BLAST+]] | 2.8.1+ | /hpc/share | modulefiles/blast | https://blast.ncbi.nlm.nih.gov | |
| | [[.:priv:cluster:softwareapplicativo: Star]] | 2.5.3a | /hpc/share | |https://github.com/alexdobin/STAR | | | [[..:priv:cluster:softwareapplicativo:barrnap]] | 0.9 | /hpc/share | modulefiles/barrnap | https://github.com/tseemann/barrnap | |
| | [[.:priv:cluster:softwareapplicativo: Bedtools ]] | 2.25.0 | /hpc/share | | http://bedtools.readthedocs.io/en/latest/ | | | [[..:priv:cluster:softwareapplicativo:HMMER]] | 3.2.1 | /hpc/share | moduledeps/gnu-openmpi/hmmer | http://hmmer.org/documentation.html | |
| | [[.:priv:cluster:softwareapplicativo: Bowtie ]] | 1.2.2 | /hpc/share | | http://bowtie-bio.sourceforge.net/index.shtml | | |
| | [[.:priv:cluster:softwareapplicativo: Bowtie2 ]] | 2.3.3.1 | /hpc/share | | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | | |
| | [[.:priv:cluster:softwareapplicativo: tensorflow-gpu ]] | | module | python/3.6.3 cuda gnu | https://www.tensorflow.org | | |
| | [[.:priv:cluster:softwareapplicativo: keras ]] | | module |python/3.6.3 cuda gnu| https://keras.io/ | | |
| | [[.:priv:cluster:softwareapplicativo: qiime ]] | | virtualenv | | http://qiime.org/ | | |
| | [[.:priv:cluster:softwareapplicativo: flash ]] | | module | | | | |
| | [[.:priv:cluster:softwareapplicativo: prinseq ]] | | module | | | | |
| | [[.:priv:cluster:softwareapplicativo: espresso md ]] | | virtualenv | | http://espressomd.org/wordpress/| | |
| | [[.:priv:cluster:softwareapplicativo: namd ]] | | module | | http://www.ks.uiuc.edu/Research/namd/| | |
| | [[.:priv:cluster:softwareapplicativo: plumed ]] | | module | | http://www.plumed.org/| | |
| | [[.:priv:cluster:softwareapplicativo: mpi4py ]] | | rpm ohpc | | | | |
