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guides:available-applications [13.10.2020 12:12] Juha Kekäläinen |
guides:available-applications [09.06.2021 14:10] (current) Administrator |
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- | #Available applications on SOLU and SAMPO servers | + | #Available applications on BIC servers |
Most of the preinstalled applications on the computing servers are installed as [environment modules](https:// | Most of the preinstalled applications on the computing servers are installed as [environment modules](https:// | ||
- | To use application you first must activate it. This will modify the [environment variables](https:// | + | To use application you first must activate it. This will modify the [environment variables](https:// |
**To find the available modules you will need to use the following command in terminal** | **To find the available modules you will need to use the following command in terminal** | ||
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This will give you an list of all the available modules. | This will give you an list of all the available modules. | ||
- | For example list of available applications (13.01.2020) below: | + | For example list of available applications |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | bamtools/2.5.1 fastqc/0.11.7 openmpi/1.10.7-2 r/3.5.3 | + | eagle/2.4.1 |
- | | + | |
- | | + | |
- | bedtools2/2.27.1 | + | |
- | bowtie/1.2.3 | + | bcftools/1.10.2 |
- | bowtie2/2.3.4.1 | + | bedops/2.4.39 fastx-toolkit/ |
- | bwa/0.7.17 | + | bedtools2/2.27.1 freebayes/1.1.0 |
- | clustalw/2.1 | + | bedtools2/2.29.2 gcc/8.2.0 |
- | cufflinks/2.2.1 | + | bowtie/1.2.3 |
- | diamond/0.9.21 | + | bowtie2/2.3.4.1 |
+ | bwa/0.7.17 | ||
+ | |||
+ | ** You can search for an package with ' | ||
+ | |||
+ | module spider homer | ||
** To activate the application you can use the following command** | ** To activate the application you can use the following command** | ||
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module load bowtie2 | module load bowtie2 | ||
- | Note that you can activate multiple applications **but** you cannot activate multiple versions of the same application. | + | Note: You can activate multiple applications **but** you cannot activate multiple versions of the same application. |
- | ** If you wish to Load some specific version number ** | + | ** If you wish to Load some specific version number |
module load bowtie2/ | module load bowtie2/ | ||
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module restore | module restore | ||
+ | Note: If you add this line to your $HOME/ | ||
- | ** You can quickly go to the application | + | ** You can quickly go to the application |
module load bowtie2 | module load bowtie2 | ||
cd $BOWTIE2_ROOT | cd $BOWTIE2_ROOT | ||
+ | | ||
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