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guides:available-applications
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In the terminal, you can see the list of available software packages by command 'modul avail'. A short list of available applications (13.01.2020) below:
bamtools/2.5.1 cufflinks/2.2.1 mothur/1.40.5 r/3.5.3 bamutil/1.0.13 datamash/1.3 openjdk/11.0.2 r/3.6.0 bcftools/1.9 diamond/0.9.21 openmpi/1.10.7-2 r/3.6.1 (D) bedtools2/2.27.1 fastqc/0.11.7 picard/2.18.3 samtools/1.9 blast-plus/2.7.1 fastx-toolkit/0.0.14 plink/1.07 sra-toolkit/2.9.2 bowtie/1.2 gcc/8.2.0 plink/1.90b6.12 (D) star/2.5.1b bowtie/1.2.3 (D) hisat2/2.1.0 prinseq-lite/0.20.4 star/2.5.4b bowtie2/2.3.4.1-python-3.7.0 hmmer/3.0 python/2.7.15 star/2.6.1b (D) breakdancer/master htslib/1.9 python/2.7.17 tabix/2013-12-16 breakdancer/1.4.5 (D) jdk/12.0.1 python/3.7.0 trimmomatic/0.36 bwa/0.7.17 matlab/R2018b python/3.7.3 (D) vcftools/0.1.14 clustalw/2.1 mono/5.4.1.7 r/3.5.1 seqan/2.4.0 kallisto/0.43.1 homer/4.9.1 homer/4.10 (D)
Lmod Module Environment
Applications are managed with the Lmod Environment Module System. Guide for the Lmod can be found here
Quick tutorial:
Available modules
module avail
Load module
module load bowtie2
If you wish to Load some specific version number
module load python/3.7.3
Unload module
module unload bowtie2
Save list of loaded modules
module save
Restore saved modules
module restore
Application location
You can quickly go to the application location by writing:
module load bowtie2 cd $BOWTIE2_ROOT
guides/available-applications.1602574433.txt.gz · Last modified: 13.10.2020 10:33 by Juha Kekäläinen