Mercurial > repos > fubar > jbrowse2dev
changeset 10:0db895a99532 draft default tip
Uploaded
| author | fubar |
|---|---|
| date | Fri, 05 Jan 2024 22:26:16 +0000 |
| parents | 6a41f87b5d7f |
| children | |
| files | jbrowse2/jbrowse2.py jbrowse2/jbrowse2.xml jbrowse2/tstar.sh |
| diffstat | 3 files changed, 49 insertions(+), 38 deletions(-) [+] |
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--- 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=[ {
--- a/jbrowse2/jbrowse2.xml Fri Jan 05 05:06:21 2024 +0000 +++ b/jbrowse2/jbrowse2.xml Fri Jan 05 22:26:16 2024 +0000 @@ -14,16 +14,12 @@ ## Copy the XML file into the directory, mostly for debugging ## but nice if users want to reproduce locally cp '$trackxml' '$output.files_path/galaxy.xml' && - -export JBROWSE_SOURCE_DIR=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && - +export JBROWSE_SOURCE_DIR=\$(dirname \$(which jbrowse)) && ## Once that's done, we run the python script to handle the real work python '$__tool_directory__/jbrowse2.py' - --jbrowse \${JBROWSE_SOURCE_DIR} - --outdir '$output.files_path' -'$trackxml' && +--xml '$trackxml' && cp '$output.files_path/index.html' '$output'