From 8f3c58092b83f19c2c899c91b7136b928d61ef15 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Tue, 26 Jun 2018 15:23:41 +0200
Subject: [PATCH] More README updates
---
README.md | 21 +++++++++++++++------
1 file changed, 15 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index 34fc78e..a1180af 100755
--- a/README.md
+++ b/README.md
@@ -78,7 +78,11 @@ of this pipeline, which can be used in Snakemake together with
1. **Singularity required.** We tested this with version 2.5.1.
- 2. **Run Snakemake with `--use-singularity` option.** The software inside the
+ 2. **Provide SNP call set (optional).** External VCF files (if available) should be
+ *copied* into a subfolder of the pipeline, which can be read from within the image.
+ Accordingly, you need to specify a relative path in `Snake.config-singularity.json`.
+
+ 3. **Run Snakemake with `--use-singularity` option.** The software inside the
Singularity image need to access external data, such as the reference genome.
These are specified in a separate config file.
@@ -104,10 +108,6 @@ of this pipeline, which can be used in Snakemake together with
> **Note:** Currently only hg38 is supported within the singularity inmage.
- 3. **SNP call set.** External VCF files (if available) should be *copied* into a
- subfolder of the pipeline, which can be read from within the image. Also specify
- a relative path in `Snake.config-singularity.json`.
-
### Option 2: Bioconda environment
@@ -158,7 +158,7 @@ In case you do not have Conda yet, it is easiest to just install
3. Run `snakemake`
-## Snakemake recommendations
+## Cluster support (experimental)
You can ask Snakemake to submit your jobs to a HPC cluster. We provided a config
file (`cluster.json`) for this purpose, yet it might need to be adapted to your
@@ -177,6 +177,15 @@ infrastructure. Here is an example command:
--latency-wait 60
```
+ In the HPC system this was tested (based on SLURM), Snakemake sometimes does not
+ recognize if a job was killed on the cluster and hangs up waiting for it to finish.
+ To overcome this, we provide a small script called `cluster_status.py` which can
+ be passed to Snakemake as shown below. Note that this script might need to be adapted.
+
+ ```
+ --cluster-status cluster_status.py
+ ```
+
Finally, of course the cluster mode can be combined with `--use-singularity`.
--
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