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Tools

module

• module avail

u227664@master01:~$ module avail

---------------------------------------------------------------- /cm/local/modulefiles ----------------------------------------------------------------
cluster-tools/7.1      cmd                    cmsh                   freeipmi/1.4.8         ipmitool/1.8.15        module-info
cluster-tools-dell/7.1 cm-scale-cluster/7.1   dot                    gcc/5.1.0              module-git             null

--------------------------------------------------------------- /cm/shared/modulefiles ----------------------------------------------------------------
5.3.1                     bowtie/1.1.2              EasyBuild                 gdb/7.9                   iozone/3_471              penncnv/1.0.3             bam-readcount/1           bowtie/2.3.3.1            ea-utils/27               genomicsimla/1.1.3        java/7.0.25               perl/5.16.3               basespace-invaders/1.0.0  bwa/0.7.15
basespace-python/1.0.0    bwa/0.7.16a               elprep/3.0                gnuplot/5.0.6             jdk/jdk1.8.0_66           perl/config-simple/4.59   samtools/0.1.19
bcftools/1.3.1            bwa/0.7.5a                elprep/3.01               go/1.9                    lapack/gcc/64/3.5.0       perl/test-simple/1,001014 samtools/1.3.1
bcl2fastq/2.17            canu/1.4                  emboss/6.6.0              hdf5/1.6.10               mothur/1.39.1             perl/time-piece/1.31      samtools/1.6
beagle/21jan17            cellranger/1.3.1          ensembl-tools/86          hdf5_18/1.8.14            nanonet/1                 picard-tools/1.78         scala/2.12.0
beagle/3.3.2              cmgui/7.1                 excelcompare/0.6.1        homer/4.9                 ncbi/eutils/2016-11-22    picard-tools/2.7.1        seqff/1
bedtools/2.17.0           crispresso/1              fastqc/0.11.5             hpl/2.1                   netperf/2.6.0             puppet/3.7.5              singularity/2.2.1

• module load

u227664@master01:~$ module load bwa/0.7.5a
u227664@master01:~$ bed <tab>

u227664@master01:~$ bedtools --version
bedtools v2.17.0

• module list

u227664@master01:~$ module list
Currently Loaded Modulefiles:
  1) fastqc/0.11.5   2) bedtools/2.17.0    3) bwa/0.7.5a

SSH

Also called Secure Shell.
It allows secured connections on remote servers.

u227664@genetic.master01 ~ $ ssh myUsername@myDestination 
u227664@genetic.master01's password:
myUsername@myDestination  ~ $

Read also: Secured authentification

lsof

• lsof -i : Verify which ports are open, and by what/who