From 3b86133f4c5716ea6167dcaecb18942abae2f042 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 19 Aug 2015 14:06:33 +0200
Subject: [PATCH] Remove env value
---
.../main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index a40a2eaba..9acf9a1dd 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -65,8 +65,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
}
/** return commandline to execute */
- def cmdLine = "BOWTIE_INDEXES=" + reference.getParent + " &&" +
- required(executable) +
+ def cmdLine = required(executable) +
optional("--threads", threads) +
conditional(sam, "--sam") +
conditional(best, "--best") +
@@ -79,7 +78,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
optional("--maxbts", maxbts) +
optional("--maqerr", maqerr) +
optional("--maxins", maxins) +
- required(reference.getName.stripSuffix(".fa").stripSuffix(".fasta")) +
+ required(reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")) +
(R2 match {
case Some(r2) =>
required("-1", R1) +
--
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