Commit 16aed941 authored by Peter Kruczkiewicz's avatar Peter Kruczkiewicz

move duplicated shovill section to _includes template

parent 4059c4fa
Pipeline #7597 canceled with stage
### Address shovill related issues
#### Error 256 from running `kmc`/`samtools`
You will need to install the correct versions of some dependencies for `kmc`/`samtools` so after installing `shovill`:
```bash
# activate the Galaxy shovill conda env
source galaxy/deps/_conda/bin/activate galaxy/deps/_conda/envs/__shovill@0.9.0
# install ncurses and bzip2 from conda-forge channel
conda install -c conda-forge ncurses bzip2
```
#### [PILON] Java/JVM heap allocation issues
[PILON] is a Java application and may require the JVM heap size to be set (e.g. `_JAVA_OPTIONS=-Xmx4g`).
If [shovill] under Galaxy submits jobs to a [SLURM] workload manager, it may be necessary to allot about 4G more through SLURM than through [shovill] `--ram` (default is `${SHOVILL_RAM:-4}` or 4G as of tool revision [57d5928f456e]) so if you give [shovill] 4G, give the SLURM job 8G.
One way you can adjust the `$SHOVILL_RAM` environment variable is via the [conda environment][]. That is, if you find the conda environment containing `shovill` you can set up files in `etc/conda/activate.d` and `etc/conda/deactivate.d` to set environment variables.
```bash
cd galaxy/deps/_conda/bin/activate galaxy/deps/_conda/envs/__shovill@0.9.0
mkdir -p etc/conda/activate.d
mkdir -p etc/conda/deactivate.d
echo -e "export _OLD_SHOVILL_RAM=\$SHOVILL_RAM\nexport SHOVILL_RAM=8" >> etc/conda/activate.d/shovill-ram.sh
echo -e "export SHOVILL_RAM=\$_OLD_SHOVILL_RAM" >> etc/conda/activate.d/shovill-ram.sh
```
You could also get fancier with this by setting `SHOVILL_RAM` based on [GALAXY_MEMORY_MB][], which is assigned by Galaxy based on your job configuration and resource requirements. For example, by setting `SHOVILL_RAM=$($GALAXY_MEMORY_MB/1024)`.
[57d5928f456e]: https://toolshed.g2.bx.psu.edu/repos/iuc/shovill/rev/57d5928f456e
[SLURM]: https://slurm.schedmd.com
[PILON]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237348/
[shovill]: https://github.com/tseemann/shovill/
[conda environment]: https://conda.io/docs/user-guide/tasks/manage-environments.html#saving-environment-variables
[GALAXY_MEMORY_MB]: https://planemo.readthedocs.io/en/latest/writing_advanced.html#developing-for-clusters-galaxy-slots-galaxy-memory-mb-and-galaxy-memory-mb-per-slot
\ No newline at end of file
......@@ -23,37 +23,7 @@ To install these tools please proceed through the following steps.
Galaxy makes use of [Conda][conda] to automatically install some dependencies for this workflow. Please verify that the version of Galaxy is >= v16.01 and has been setup to use conda (by modifying the appropriate configuration settings, see [here][galaxy-config] for additional details). A method to get this workflow to work with a Galaxy version < v16.01 is available in [FAQ/Conda dependencies][].
### Address shovill related issues
#### Error 256 from running `kmc`/`samtools`
You will need to install the correct versions of some dependencies for `kmc`/`samtools` so after installing `shovill`:
```bash
# activate the Galaxy shovill conda env
source galaxy/deps/_conda/bin/activate galaxy/deps/_conda/envs/__shovill@0.9.0
# install ncurses and bzip2 from conda-forge channel
conda install -c conda-forge ncurses bzip2
```
#### [PILON] Java/JVM heap allocation issues
[PILON] is a Java application and may require the JVM heap size to be set (e.g. `_JAVA_OPTIONS=-Xmx4g`).
If [shovill] under Galaxy submits jobs to a [SLURM] workload manager, it may be necessary to allot about 4G more through SLURM than through [shovill] `--ram` (default is `${SHOVILL_RAM:-4}` or 4G as of tool revision [57d5928f456e]) so if you give [shovill] 4G, give the SLURM job 8G.
One way you can adjust the `$SHOVILL_RAM` environment variable is via the [conda environment][]. That is, if you find the conda environment containing `shovill` you can set up files in `etc/conda/activate.d` and `etc/conda/deactivate.d` to set environment variables.
```bash
cd galaxy/deps/_conda/bin/activate galaxy/deps/_conda/envs/__shovill@0.9.0
mkdir -p etc/conda/activate.d
mkdir -p etc/conda/deactivate.d
echo -e "export _OLD_SHOVILL_RAM=\$SHOVILL_RAM\nexport SHOVILL_RAM=8" >> etc/conda/activate.d/shovill-ram.sh
echo -e "export SHOVILL_RAM=\$_OLD_SHOVILL_RAM" >> etc/conda/activate.d/shovill-ram.sh
```
You could also get fancier with this by setting `SHOVILL_RAM` based on [GALAXY_MEMORY_MB][], which is assigned by Galaxy based on your job configuration and resource requirements. For example, by setting `SHOVILL_RAM=$($GALAXY_MEMORY_MB/1024)`.
{% include administrator/galaxy/pipelines/shovill.md %}
## Step 2: Install Galaxy Tools
......
......@@ -22,37 +22,7 @@ To install these tools please proceed through the following steps.
Galaxy makes use of [Conda][conda] to automatically install some dependencies for this workflow. Please verify that the version of Galaxy is >= v16.01 and has been setup to use conda (by modifying the appropriate configuration settings, see [here][galaxy-config] for additional details). A method to get this workflow to work with a Galaxy version < v16.01 is available in [FAQ/Conda dependencies][].
### Address shovill related issues
#### Error 256 from running `kmc`/`samtools`
You will need to install the correct versions of some dependencies for `kmc`/`samtools` so after installing `shovill`:
```bash
# activate the Galaxy shovill conda env
source galaxy/deps/_conda/bin/activate galaxy/deps/_conda/envs/__shovill@0.9.0
# install ncurses and bzip2 from conda-forge channel
conda install -c conda-forge ncurses bzip2
```
#### [PILON] Java/JVM heap allocation issues
[PILON] is a Java application and may require the JVM heap size to be set (e.g. `_JAVA_OPTIONS=-Xmx4g`).
If [shovill] under Galaxy submits jobs to a [SLURM] workload manager, it may be necessary to allot about 4G more through SLURM than through [shovill] `--ram` (default is `${SHOVILL_RAM:-4}` or 4G as of tool revision [57d5928f456e]) so if you give [shovill] 4G, give the SLURM job 8G.
One way you can adjust the `$SHOVILL_RAM` environment variable is via the [conda environment][]. That is, if you find the conda environment containing `shovill` you can set up files in `etc/conda/activate.d` and `etc/conda/deactivate.d` to set environment variables.
```bash
cd galaxy/deps/_conda/bin/activate galaxy/deps/_conda/envs/__shovill@0.9.0
mkdir -p etc/conda/activate.d
mkdir -p etc/conda/deactivate.d
echo -e "export _OLD_SHOVILL_RAM=\$SHOVILL_RAM\nexport SHOVILL_RAM=8" >> etc/conda/activate.d/shovill-ram.sh
echo -e "export SHOVILL_RAM=\$_OLD_SHOVILL_RAM" >> etc/conda/activate.d/shovill-ram.sh
```
You could also get fancier with this by setting `SHOVILL_RAM` based on [GALAXY_MEMORY_MB][], which is assigned by Galaxy based on your job configuration and resource requirements. For example, by setting `SHOVILL_RAM=$($GALAXY_MEMORY_MB/1024)`.
{% include administrator/galaxy/pipelines/shovill.md %}
## Step 2: Install Galaxy Tools
......
......@@ -20,36 +20,7 @@ To install these tools please proceed through the following steps.
Galaxy makes use of [Conda][conda] to automatically install some dependencies for SISTR. Please verify that the version of Galaxy is >= v16.01 and has been setup to use conda (by modifying the appropriate configuration settings, see [here][galaxy-config] for additional details). A method to get SISTR to work with a Galaxy version < v16.01 is available in [FAQ/Conda dependencies][].
### Address shovill related issues
#### Error 256 from running `kmc`/`samtools`
You will need to install the correct versions of some dependencies for `kmc`/`samtools` so after installing `shovill`:
```bash
# activate the Galaxy shovill conda env
source galaxy/deps/_conda/bin/activate galaxy/deps/_conda/envs/__shovill@0.9.0
# install ncurses and bzip2 from conda-forge channel
conda install -c conda-forge ncurses bzip2
```
#### [PILON] Java/JVM heap allocation issues
[PILON] is a Java application and may require the JVM heap size to be set (e.g. `_JAVA_OPTIONS=-Xmx4g`).
If [shovill] under Galaxy submits jobs to a [SLURM] workload manager, it may be necessary to allot about 4G more through SLURM than through [shovill] `--ram` (default is `${SHOVILL_RAM:-4}` or 4G as of tool revision [57d5928f456e]) so if you give [shovill] 4G, give the SLURM job 8G.
One way you can adjust the `$SHOVILL_RAM` environment variable is via the [conda environment][]. That is, if you find the conda environment containing `shovill` you can set up files in `etc/conda/activate.d` and `etc/conda/deactivate.d` to set environment variables.
```bash
cd galaxy/deps/_conda/bin/activate galaxy/deps/_conda/envs/__shovill@0.9.0
mkdir -p etc/conda/activate.d
mkdir -p etc/conda/deactivate.d
echo -e "export _OLD_SHOVILL_RAM=\$SHOVILL_RAM\nexport SHOVILL_RAM=8" >> etc/conda/activate.d/shovill-ram.sh
echo -e "export SHOVILL_RAM=\$_OLD_SHOVILL_RAM" >> etc/conda/activate.d/shovill-ram.sh
```
You could also get fancier with this by setting `SHOVILL_RAM` based on [GALAXY_MEMORY_MB][], which is assigned by Galaxy based on your job configuration and resource requirements. For example, by setting `SHOVILL_RAM=$($GALAXY_MEMORY_MB/1024)`.
{% include administrator/galaxy/pipelines/shovill.md %}
## Step 2: Install Galaxy Tools
......
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