From 4efe9eb016c29bc696bae941d80595a32a19f15b Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 29 Jul 2020 13:59:49 +0200
Subject: [PATCH] let valet use only one thread for samtools sort

with `-@ 16` I get `samtools sort: couldn't allocate memory for bam_mem`

seem better anyway with restrictive HPC setups
---
 recipes/valet/meta.yaml   |  2 +-
 recipes/valet/valet.patch | 19 ++++++++++++++-----
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/recipes/valet/meta.yaml b/recipes/valet/meta.yaml
index 115f98d4782ab..e97f461dd80bb 100644
--- a/recipes/valet/meta.yaml
+++ b/recipes/valet/meta.yaml
@@ -14,7 +14,7 @@ source:
 
 build:
   noarch: generic
-  number: 2
+  number: 3
 
 requirements:
   run:
diff --git a/recipes/valet/valet.patch b/recipes/valet/valet.patch
index 557e7dbeea00a..fc2577651b455 100644
--- a/recipes/valet/valet.patch
+++ b/recipes/valet/valet.patch
@@ -1,11 +1,20 @@
---- a/src/py/valet.py
-+++ b/src/py/valet.py
-@@ -13,7 +13,7 @@ import sys
+--- src/py/valet.py	2017-08-01 23:04:55.000000000 +0200
++++ src/py/valet.py	2020-07-29 13:56:29.524490605 +0200
+@@ -13,7 +13,7 @@
  import subprocess
  from subprocess import Popen, PIPE
-
+ 
 -BASE_PATH = os.path.dirname(sys.argv[0])[:-len('src/py/')]
 +BASE_PATH = os.path.dirname(os.path.realpath(__file__))[:-len('src/py/')]
  FILE_LIMIT = resource.getrlimit(resource.RLIMIT_NOFILE)[1]
  FNULL = open('/dev/null', 'w')
- COMMANDS_FILE = None
\ No newline at end of file
+ COMMANDS_FILE = None
+@@ -524,7 +524,7 @@
+     call_arr = ["samtools", "view", "-F", "0x100", "-bS", sam_output_location]
+     run(call_arr, bam_fp, error_fp)
+ 
+-    call_arr = ["samtools", "sort", "-@ 16", "-o", sorted_bam_location+".bam", bam_location]
++    call_arr = ["samtools", "sort", "-o", sorted_bam_location+".bam", bam_location]
+     run(call_arr, stderr=FNULL)
+ 
+     coverage_file_dir = output_dir + "/coverage/"