fixed hisat2_extract.. issue with exact path

mshakya · Jul 10, 2017 · 24cb950 · 24cb950
1 parent 08ad143
commit 24cb950
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,4 +7,5 @@ bin/bowtie2
 bin/htseq-count
 PyPiReT.sublime-workspace
 .cache/
-thirdParty/JBrowse-1.11.6/*.*
+thirdParty/JBrowse-1.11.6/*.*
+sftp-config.json
diff --git a/pypiret/Runs/Map.py b/pypiret/Runs/Map.py
@@ -174,19 +174,19 @@ def program_args(self):
                     gff.split("/")[-1].split(".")[0] + ".gtf"
                 out_file = self.workdir + "/" +\
                     gff.split("/")[-1].split(".")[0] + ".splice"
-            return ["hisat2_extract_splice_sites.py",
+            return [self.bindir + "/../scripts/hisat2_extract_splice_sites.py",
                     "-i", gtf_file, "-o", out_file]
         else:
             gtf_file = self.workdir + "/" +\
                 self.gff_file.split("/")[-1].split(".")[0] + ".gtf"
 
-            return ["hisat2_extract_splice_sites.py",
+            return [self.bindir + "/../scripts/hisat2_extract_splice_sites.py",
                     "-i", gtf_file, "-o", self.workdir + "/" +
                     self.gff_file.split("/")[-1].split(".")[0] + ".splice"]
 
     def program_environment(self):
         """Environmental variables for this program."""
-        return {'PATH': + self.bindir + "../scripts" + ":" + os.environ["PATH"]}
+        return {'PATH': self.bindir + "/../scripts/" + ":" + os.environ["PATH"]}
 
 
 # @inherits(FastQC.PairedRunQC)