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hpc:applications_and_libraries [2023/10/13 15:32] Adrien Albert [Variant Effect Predictor (VEP)] |
hpc:applications_and_libraries [2024/03/25 16:52] (current) Adrien Albert [Pull an existing image] |
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|foss/2022b |gcc 12.2.0 |openmpi 4.1.4 | | |foss/2022b |gcc 12.2.0 |openmpi 4.1.4 | | ||
|foss/2023a |gcc 12.3.0 |openmpi 4.1.5 | | |foss/2023a |gcc 12.3.0 |openmpi 4.1.5 | | ||
+ | |foss/2023b |gcc 13.2.0 |openmpi 4.1.6 | | ||
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capello@login2: | capello@login2: | ||
</ | </ | ||
+ | |||
===== Jupyter notebook and Jupyter lab===== | ===== Jupyter notebook and Jupyter lab===== | ||
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~/ | ~/ | ||
</ | </ | ||
+ | |||
+ | ==== Pip install from source ==== | ||
+ | By default when you use '' | ||
+ | |||
+ | Example to build hpy from source. The '' | ||
+ | < | ||
+ | pip install --no-binary h5py h5py | ||
+ | </ | ||
+ | |||
===== R project and RStudio ===== | ===== R project and RStudio ===== | ||
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===== Variant Effect Predictor (VEP) ===== | ===== Variant Effect Predictor (VEP) ===== | ||
+ | |||
+ | This tutorials is inspired from VEP documentation: | ||
According vep maintainers (https:// | According vep maintainers (https:// | ||
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srun mkdir vep_data | srun mkdir vep_data | ||
srun singularity exec vep.sif INSTALL.pl -c vep_data -a p -g all -r vep_data | srun singularity exec vep.sif INSTALL.pl -c vep_data -a p -g all -r vep_data | ||
- | srun mkdir -p $HOME/ | + | srun mkdir -p $HOME/ |
- | srun mv * $HOME/ | + | srun mv * $HOME/ |
</ | </ | ||
==== Install species | ==== Install species | ||
- | To download species after the installation run (it assumes you have the same directory arch as above): | + | To download species after the installation run the following cmd line(it assumes you have the same directory arch as above):\\ |
- | //It ran the command | + | //It ran the install |
- | + | | |
- | srun singularity exec vep.sif INSTALL.pl -c vep_data -a cf -s < | + | |
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==== Intro ==== | ==== Intro ==== | ||
- | Apptainer is a Docker like for HPC. It is available directly on the OS, not through module. | + | Apptainer is a Docker like for HPC. It is available directly on the OS, not through module. |
+ | As you don't have root access on Baobab, you cannot build recipe file on Baobab. If you need to do this, you may want to build the image on your own machine and transfer the image to Baobab.\\ | ||
+ | You can download existing images from shub (singularity hub) or from docker (docker public or private registry).\\ | ||
+ | The image will be converted to a read-only squashfs on Baobab disk. It's not possible to have writable images as user. Instead you should build the image as sandbox.\\ | ||
- | As you don't have root access on Baobab, you cannot build recipe file on Baobab. If you need to do this, you may want to build the image on your own machine and transfer the image to Baobab. | + | Apptainer images are immutable, but it is possible |
- | You can download | + | === Pull an existing |
+ | <WRAP round alert 50%> | ||
+ | Do not run the following commands on login node !! It's using too much cpu | ||
+ | </ | ||
+ | Exemple with Rstudio: | ||
- | The image will be converted to a read-only squashfs on Baobab disk. It's not possible to have writable images as user. Instead you should build the image as sandbox. | + | **Create |
- | + | (baobab)-[alberta@login2 ~]$ MYPROJECT=" | |
- | Apptainer images are immutable, but it is possible to append an overlay, see below. | + | (baobab)-[alberta@login2 ~]$ mkdir -p singularity/ |
+ | (baobab)-[alberta@login2 ~]$ cd !$ | ||
+ | (baobab)-[alberta@login2 rocker]$ salloc --partition=shared-cpu --time=00: | ||
+ | (baobab)-[alberta@cpu300 rocker]$ apptainer pull docker:// | ||
+ | | ||
+ | | ||
+ | And Voila; I get my sif image rstudio_4.2.sif | ||
==== Convert a Docker image ==== | ==== Convert a Docker image ==== | ||