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authorJustin Bedo <cu@cua0.org>2020-11-18 07:44:19 +1100
committerJustin Bedo <cu@cua0.org>2020-11-18 07:44:19 +1100
commit233b915bd2bfe8abe302874f7b7467ad39048a2c (patch)
tree3903a204a0b5569a8c4478b229ece0658ada06b2 /examples
parenteede5717879062ef0cebde2a5718725e7afd17ca (diff)
rewrite cluster example to usse overlay
Diffstat (limited to 'examples')
-rw-r--r--examples/ex-tnpair/cluster.nix49
1 files changed, 27 insertions, 22 deletions
diff --git a/examples/ex-tnpair/cluster.nix b/examples/ex-tnpair/cluster.nix
index d7537b2..8d54995 100644
--- a/examples/ex-tnpair/cluster.nix
+++ b/examples/ex-tnpair/cluster.nix
@@ -1,25 +1,30 @@
-{ bionix ? import <bionix> { }, tmpDir ? null }:
+{ tmpDir ? null }:
let
- bionix' = (bionix."${if tmpDir == null then "slurm" else "qsub"}" {
- ppn = 24;
- mem = 7;
- walltime = "3:00:00";
- } // bionix.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; }).extend
- (self: super:
- with self; {
- minimap2.align = def super.minimap2.align {
- mem = 15;
- walltime = "16:00:00";
- };
- samtools = super.samtools // (with super.samtools; {
- markdup = def markdup { walltime = "12:00:00"; };
- fixmate = def fixmate { walltime = "10:00:00"; };
- sort = def sort {
- mem = 27;
- flags = "-m 1G";
- };
- });
- });
+ bionix = import <bionix> {
+ overlays = [
+ (_: super:
+ super."${if tmpDir == null then "slurm" else "qsub"}" {
+ ppn = 24;
+ mem = 7;
+ walltime = "3:00:00";
+ } // super.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; })
-in import ./. { bionix = bionix'; }
+ (self: super:
+ with super; {
+ minimap2.align = def minimap2.align {
+ mem = 15;
+ walltime = "16:00:00";
+ };
+ samtools = with samtools; {
+ markdup = def markdup { walltime = "12:00:00"; };
+ fixmate = def fixmate { walltime = "10:00:00"; };
+ sort = def sort {
+ mem = 27;
+ flags = "-m 1G";
+ };
+ };
+ })
+ ];
+ };
+in import ./. { inherit bionix; }