Merge pull request #53 from sanger-tol/longranger_config

Longranger config
sanger-tol · Aug 16, 2024 · 76d3fc9 · 76d3fc9
2 parents bbdf389 + aab1b30
commit 76d3fc9
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diff --git a/conf/longranger_lsf_sanger.config b/conf/longranger_lsf_sanger.config
@@ -5,13 +5,18 @@
 */
 
 process {
+    withName: LONGRANGER_MKREF {
+        container = "gitlab-registry.internal.sanger.ac.uk/tol-it/software/docker-images/longranger:2.2.2-c4"
+    }
+
     withName: LONGRANGER_ALIGN {
+        container = "gitlab-registry.internal.sanger.ac.uk/tol-it/software/docker-images/longranger:2.2.2-c4"
         // Same arguments as in conf/modules.config but with the LSF job mode
         ext.args = "--disable-ui --nopreflight --jobmode=lsf"
     }
 }
 
 // Make the LSF configuration available to the container / longranger
 singularity.envWhitelist = "LSF_BINDIR,LSF_SERVERDIR,LSF_LIBDIR,LSF_ENVDIR"
-singularity.runOptions   = "-B ${projectDir}/assets/martian.lsf.template:/opt/longranger-2.2.2/martian-cs/2.3.2/jobmanagers/lsf.template -B /software -B /etc/lsf.conf --env APPEND_PATH=$LSF_BINDIR:$LSF_SERVERDIR:/software/singularity-v3.9.0/bin"
+singularity.runOptions   = "-B ${projectDir}/assets/martian.lsf.template:/opt/longranger-2.2.2/martian-cs/2.3.2/jobmanagers/lsf.template -B /software -B /etc/lsf.conf --env APPEND_PATH=$LSF_BINDIR:$LSF_SERVERDIR:/software/singularity/3.11.4/bin"
 
diff --git a/docs/usage.md b/docs/usage.md
@@ -76,6 +76,45 @@ mito:
 ```
 </details>
 
+## Extra installation procedures
+
+### Longranger
+
+Longranger is a proprietary software product from 10X Genomics.
+Its terms and conditions state that we _cannot_ redistribute the copy we have in the Tree of Life department.
+
+If you want to run the polising option, you have to install longranger yourself.
+Go to <https://support.10xgenomics.com/genome-exome/software/downloads/latest>,
+read their End User Software License Agreement,
+and you'll be able to download the software if you accept it.
+
+To make a Docker (or Singularity) container out of it,
+use the following Dockerfile.
+
+```Dockerfile
+FROM ubuntu:22.04
+LABEL org.opencontainers.image.licenses="10x Genomics End User Software License Agreement - https://support.10xgenomics.com/genome-exome/software/downloads/latest"
+ARG DEST=/opt
+ADD ./longranger-2.2.2.tar.gz $DEST
+RUN ln -s $DEST/longranger-2.2.2/longranger /usr/local/bin/
+```
+
+Then, to use the container in the pipeline, write the following to a `longranger.config` file
+
+```
+process {
+    withName: LONGRANGER_MKREF {
+        container = "/path/to/longranger_container"
+    }
+
+    withName: LONGRANGER_ALIGN {
+        container = "/path/to/longranger_container"
+    }
+}
+```
+
+And pass it to the pipeline with `-c longranger.config`.
+
 ## Usage
 
 ### Local testing

diff --git a/modules/local/longranger/align/main.nf b/modules/local/longranger/align/main.nf
@@ -7,8 +7,6 @@ process LONGRANGER_ALIGN {
 
     def version = '2.2.2-c4'
 
-    container "gitlab-registry.internal.sanger.ac.uk/tol-it/software/docker-images/longranger:2.2.2-c4"
-
     input:
     tuple val(meta), path(reference)
     path(fastqs, stageAs: "10X_inputs/*")

diff --git a/modules/local/longranger/mkref/main.nf b/modules/local/longranger/mkref/main.nf
@@ -4,8 +4,6 @@ process LONGRANGER_MKREF {
 
     def version = '2.2.2-c4'
 
-    container "gitlab-registry.internal.sanger.ac.uk/tol-it/software/docker-images/longranger:2.2.2-c4"
-
     input:
     tuple val(meta), path(reference)
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,8 +4,6 @@ process LONGRANGER_MKREF { @@
         def version = '2.2.2-c4'
-        container "gitlab-registry.internal.sanger.ac.uk/tol-it/software/docker-images/longranger:2.2.2-c4"
         input:
         tuple val(meta), path(reference)
@@ Expand Down @@