From 50a5153070987c5d74bfd6ed3d4e2c96c36ad9d5 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 23 Oct 2017 08:43:45 -0500
Subject: [PATCH] Add in tmp directory.
---
workflow/conf/install_R_packages.R | 7 +++++++
workflow/scripts/map_qc.py | 4 ++--
2 files changed, 9 insertions(+), 2 deletions(-)
create mode 100644 workflow/conf/install_R_packages.R
diff --git a/workflow/conf/install_R_packages.R b/workflow/conf/install_R_packages.R
new file mode 100644
index 0000000..5641c4f
--- /dev/null
+++ b/workflow/conf/install_R_packages.R
@@ -0,0 +1,7 @@
+install.packages("snow", repos="http://cran.us.r-project.org")
+install.packages("snowfall", repos="http://cran.us.r-project.org")
+install.packages("bitops", repos="http://cran.us.r-project.org")
+install.packages("caTools", repos="http://cran.us.r-project.org")
+source("http://bioconductor.org/biocLite.R")
+biocLite("Rsamtools",suppressUpdates=TRUE)
+install.packages("../../phantompeakqualtools/spp_1.14.tar.gz")
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index e33035f..4451d91 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -158,8 +158,8 @@ def dedup_mapped(bam, bam_basename, paired):
" --overflow-list-size=20000000 --io-buffer-size=256"
with open(dup_file_qc_filename, 'w') as fh:
sambamba_markdup_command = (
- "sambamba markdup -t %d %s %s %s"
- % (cpu_count(), sambamba_params, bam, tmp_dup_mark_filename)
+ "sambamba markdup -t %d %s --tmpdir=%s %s %s"
+ % (cpu_count(), sambamba_params, os.getcwd(), bam, tmp_dup_mark_filename)
)
logger.info(sambamba_markdup_command)
subprocess.check_call(
--
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