diff jbrowse2/jbrowse2.py @ 10:0db895a99532 draft default tip

Uploaded

--- a/jbrowse2/jbrowse2.py	Fri Jan 05 05:06:21 2024 +0000
+++ b/jbrowse2/jbrowse2.py	Fri Jan 05 22:26:16 2024 +0000
@@ -108,19 +108,18 @@
 
 
 class JbrowseConnector(object):
-    def __init__(self, jbrowse, outdir, genomes):
+    def __init__(self, outdir, genomes):
         self.debug = False
         self.usejson = True
         self.giURL = GALAXY_INFRASTRUCTURE_URL
-        self.jbrowse = jbrowse
         self.outdir = outdir
         os.makedirs(self.outdir, exist_ok=True)
         self.genome_paths = genomes
         self.trackIdlist = []
         self.tracksToAdd = []
         self.config_json = {}
-        self.config_json_file = os.path.realpath(os.path.join(outdir, "config.json"))
-        self.clone_jbrowse(self.jbrowse, self.outdir)
+        self.config_json_file = os.path.join(outdir, "config.json")
+        self.clone_jbrowse(destination=self.outdir)
 
     def subprocess_check_call(self, command, output=None):
         if output:
@@ -133,9 +132,10 @@
 
     def subprocess_popen(self, command):
         if self.debug:
-            log.debug("cd %s && %s", self.outdir, command)
+            log.debug(command)
         p = subprocess.Popen(
             command,
+            cwd=self.outdir,
             shell=True,
             stdin=subprocess.PIPE,
             stdout=subprocess.PIPE,
@@ -144,19 +144,16 @@
         output, err = p.communicate()
         retcode = p.returncode
         if retcode != 0:
-            log.error("cd %s && %s", self.outdir, command)
+            log.error(command)
             log.error(output)
             log.error(err)
             raise RuntimeError("Command failed with exit code %s" % (retcode))
 
     def subprocess_check_output(self, command):
         if self.debug:
-            log.debug("cd %s && %s", self.outdir, " ".join(command))
+            log.debug(" ".join(command))
         return subprocess.check_output(command, cwd=self.outdir)
 
-    def _jbrowse_bin(self, command):
-        return os.path.realpath(os.path.join(self.jbrowse, "bin", command))
-
     def symlink_or_copy(self, src, dest):
         if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool(
             os.environ["GALAXY_JBROWSE_SYMLINKS"]
@@ -175,13 +172,16 @@
             genome_name = genome_node["meta"]["dataset_dname"].strip().split()[0]
             fapath = genome_node["path"]
             faname = genome_name + ".fa.gz"
-            fadest = os.path.realpath(os.path.join(self.outdir, faname))
-            cmd = "bgzip -i -c %s > %s && samtools faidx %s" % (
+            fadest = os.path.join(self.outdir, faname)
+            # 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,
+                fadest,
             )
-            log.info("### cmd = %s" % ' '.join(cmd))
+            if self.debug:
+                log.info("### cmd = %s" % cmd)
             self.subprocess_popen(cmd)
             adapter = {
                 "type": "BgzipFastaAdapter",
@@ -275,7 +275,7 @@
             dsId,
         )
         hname = trackData["name"]
-        dest = os.path.realpath(os.path.join(self.outdir, hname))
+        dest = os.path.join(self.outdir, hname)
         url = hname
         cmd = ["cp", data, dest]
         self.subprocess_check_call(cmd)
@@ -330,7 +330,7 @@
         }
         tId = trackData["label"]
         fname = "%s.bed" % tId
-        dest = os.path.realpath("%s/%s" % (self.outdir, fname))
+        dest = "%s/%s" % (self.outdir, fname)
         # self.symlink_or_copy(data, dest)
         # Process MAF to bed-like. Need build to munge chromosomes
         gname = self.genome_name
@@ -413,7 +413,7 @@
             shutil.copy(gff3_rebased.name, gff3)
             os.unlink(gff3_rebased.name)
         url = "%s.gff3" % trackData["label"]
-        dest = os.path.realpath("%s/%s" % (self.outdir, url))
+        dest = "%s/%s" % (self.outdir, url)
         self._sort_gff(gff3, dest)
         url = url + ".gz"
         tId = trackData["label"]
@@ -467,7 +467,7 @@
 
     def add_bigwig(self, data, trackData):
         url = "%s.bw" % trackData["name"]
-        dest = os.path.realpath(os.path.join(self.outdir, url))
+        dest = os.path.join(self.outdir, url)
         cmd = ["cp", data, dest]
         self.subprocess_check_call(cmd)
         bwloc = {"uri": url}
@@ -514,7 +514,7 @@
     def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
         tId = trackData["label"]
         fname = "%s.bam" % trackData["label"]
-        dest = os.path.realpath("%s/%s" % (self.outdir, fname))
+        dest = "%s/%s" % (self.outdir, fname)
         url = fname
         self.subprocess_check_call(["cp", data, dest])
         log.info("### copied %s to %s" % (data, dest))
@@ -578,7 +578,7 @@
             trackData["metadata"]["dataset_id"],
         )
         url = "%s.vcf.gz" % tId
-        dest = os.path.realpath("%s/%s" % (self.outdir, url))
+        dest = "%s/%s" % (self.outdir, url)
         cmd = "bgzip -c %s  > %s" % (data, dest)
         self.subprocess_popen(cmd)
         cmd = ["tabix", "-p", "vcf", dest]
@@ -657,7 +657,7 @@
 
     def add_gff(self, data, ext, trackData):
         url = "%s.%s" % (trackData["label"], ext)
-        dest = os.path.realpath("%s/%s" % (self.outdir, url))
+        dest = "%s/%s" % (self.outdir, url)
         self._sort_gff(data, dest)
         url = url + ".gz"
         tId = trackData["label"]
@@ -708,7 +708,7 @@
 
     def add_bed(self, data, ext, trackData):
         url = "%s.%s" % (trackData["label"], ext)
-        dest = os.path.realpath("%s/%s.gz" % (self.outdir, url))
+        dest = "%s/%s.gz" % (self.outdir, url)
         self._sort_bed(data, dest)
         tId = trackData["label"]
         url = url + ".gz"
@@ -860,9 +860,9 @@
             else:
                 log.warn("Do not know how to handle %s", dataset_ext)
 
-    def clone_jbrowse(self, jbrowse_dir, destination):
+    def clone_jbrowse(self, destination):
         """Clone a JBrowse directory into a destination directory."""
-        cmd = ["jbrowse", "create", "-f", self.outdir]
+        cmd = ["jbrowse", "create", "-f", os.path.realpath(destination)]
         self.subprocess_check_call(cmd)
         for fn in [
             "asset-manifest.json",
@@ -874,20 +874,36 @@
         ]:
             cmd = ["rm", "-rf", os.path.join(self.outdir, fn)]
             self.subprocess_check_call(cmd)
-        cmd = ['cp', os.path.join(INSTALLED_TO, "servejb2.py"), self.outdir]
+        cmd = ["cp", os.path.join(INSTALLED_TO, "servejb2.py"), self.outdir]
+        self.subprocess_check_call(cmd)
+
+    def clone_jbrowse2(self, jbrowse_dir, destination):
+        """Clone a JBrowse directory into a destination directory."""
+        cmd = ["cp", "-rv", jbrowse_dir + "/*", self.outdir]
+        self.subprocess_check_call(cmd)
+        for fn in [
+            "asset-manifest.json",
+            "favicon.ico",
+            "robots.txt",
+            "umd_plugin.js",
+            "version.txt",
+            "test_data",
+        ]:
+            cmd = ["rm", "-rf", os.path.join(self.outdir, fn)]
+            self.subprocess_check_call(cmd)
+        cmd = ["cp", os.path.join(INSTALLED_TO, "servejb2.py"), self.outdir]
         self.subprocess_check_call(cmd)
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="", epilog="")
-    parser.add_argument("xml", type=argparse.FileType("r"), help="Track Configuration")
-
-    parser.add_argument("--jbrowse", help="Folder containing a jbrowse release")
+    parser.add_argument("--xml", help="Track Configuration")
+    parser.add_argument("--jbrowse", help="Output from 'which jbrowse'")
     parser.add_argument("--outdir", help="Output directory", default="out")
-    parser.add_argument("--version", "-V", action="version", version="%(prog)s 0.8.0")
+    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1")
     args = parser.parse_args()
 
-    tree = ET.parse(args.xml.name)
+    tree = ET.parse(args.xml)
     root = tree.getroot()
 
     # This should be done ASAP
@@ -897,9 +913,7 @@
         # so we'll prepend `http://` and hope for the best. Requests *should*
         # be GET and not POST so it should redirect OK
         GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
-
     jc = JbrowseConnector(
-        jbrowse=args.jbrowse,
         outdir=args.outdir,
         genomes=[
             {