--- a/jbrowse2.py	Thu Oct 17 11:58:53 2024 +0000
+++ b/jbrowse2.py	Fri Oct 18 11:57:55 2024 +0000
@@ -446,7 +446,7 @@
         p = subprocess.Popen(
             command,
             cwd=self.outdir,
-            shell=True,
+            shell=False,
             stdin=subprocess.PIPE,
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE,
@@ -554,13 +554,11 @@
         else:
             faname = gname + ".fa.gz"
             fadest = os.path.realpath(os.path.join(self.outdir, faname))
-            cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
-                fapath,
-                fadest,
-                fadest,
-                fadest,
-            )
-            self.subprocess_popen(cmd)
+            cmd = ["bgzip", "-i", "-c", fapath, "-I", fadest + ".gzi"]
+            with open(fadest, "wb") as fout:
+                self.subprocess_check_call(cmd, output=fout)
+            cmd = ["samtools", "faidx", fadest]
+            self.subprocess_check_call(cmd)
             contig = open(fadest + ".fai", "r").readline().strip()
         adapter = {
             "type": "BgzipFastaAdapter",
@@ -957,8 +955,9 @@
         else:
             url = tId
             dest = os.path.join(self.outdir, url)
-            cmd = "bgzip -c %s  > %s" % (data, dest)
-            self.subprocess_popen(cmd)
+            cmd = ["bgzip", "-c", data]
+            with open(dest, "wb") as fout:
+                subprocess.run(cmd, stdout=fout)
             cmd = ["tabix", "-f", "-p", "vcf", dest]
             self.subprocess_check_call(cmd)
         trackDict = {
@@ -1001,18 +1000,20 @@
     def _sort_gff(self, data, dest):
         # Only index if not already done
         if not os.path.exists(dest):
-            cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % (
-                data,
-                dest,
-            )
-            self.subprocess_popen(cmd)
+            e = os.environ
+            e['SHELL'] = '/bin/sh'
+            cmd = ['/bin/sh', '-c', "jbrowse sort-gff %s | bgzip -c > %s" % (data, dest)]
+            subprocess.run(cmd, env=e)
             self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest])
 
     def _sort_bed(self, data, dest):
         # Only index if not already done
         if not os.path.exists(dest):
-            cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest)
-            self.subprocess_popen(cmd)
+            cmd = ["sort", "-k1,1", "-k2,2n", data]
+            ps = subprocess.run(cmd, check=True, capture_output=True)
+            cmd = ["bgzip", "-c"]
+            with open(dest, "wb") as fout:
+                subprocess.run(cmd, input=ps.stdout, stdout=fout)
             cmd = ["tabix", "-f", "-p", "bed", dest]
             self.subprocess_check_call(cmd)
 
@@ -1130,7 +1131,7 @@
         self.trackIdlist.append(tId)
 
     def add_paf(self, data, trackData, pafOpts, **kwargs):
-        canPIF = False
+        canPIF = True
         tname = trackData["name"]
         tId = trackData["label"]
         url = tId
@@ -1138,11 +1139,15 @@
         useuri = data.startswith("http://") or data.startswith("https://")
         if not useuri:
             if canPIF:
-                fakeName = '%s.paf' % tId
+                fakeName = "%s.paf" % tId
                 url = "%s.pif.gz" % tId
                 cmd = ["cp", data, fakeName]
                 self.subprocess_check_call(cmd)
-                cmd = ["jbrowse", "make-pif", fakeName]  # jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
+                cmd = [
+                    "jbrowse",
+                    "make-pif",
+                    fakeName,
+                ]  # jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
                 self.subprocess_check_call(cmd)
                 usePIF = True
             else: