| Previous changeset 49:7e867ff86e44 (2024-03-07) Next changeset 51:e18f2d6c4dbe (2024-03-07) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 |
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modified:
jb2_webserver.py jbrowse2.py readme.rst |
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removed:
klBraLanc5.haps_combined.decontam.20230620.fasta.fa.gz more |
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| diff -r 7e867ff86e44 -r f350467f9433 jb2_webserver.py --- a/jb2_webserver.py Thu Mar 07 00:27:48 2024 +0000 +++ b/jb2_webserver.py Thu Mar 07 04:51:43 2024 +0000 |
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| @@ -38,12 +38,11 @@ import os import re import socketserver -import ssl import webbrowser from http.server import SimpleHTTPRequestHandler -DEFAULT_PORT = 8443 +DEFAULT_PORT = 8081 def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024): @@ -154,17 +153,6 @@ class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer): allow_reuse_address = True - def server_bind(self): - ctx = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT) - ctx.load_cert_chain('cert.pem', 'key.pem') - socketserver.TCPServer.server_bind(self) - self.socket = ctx.wrap_socket( self.socket, server_hostname = "127.0.0.1", server_side=False,) - - - def get_request(self): - (socket, addr) = socketserver.TCPServer.get_request(self) - socket.do_handshake() - return (socket, addr) if __name__ == "__main__": parser = argparse.ArgumentParser( @@ -184,16 +172,16 @@ parser.add_argument( "--bind", default="127.0.0.1", - help="IP address to bind to (default: 127.0.0.1)", + help="IP address to bind to (default: 127.0.0.1 - use 0.0.0.0 to allow access on your network)", ) args = parser.parse_args() handler = functools.partial(RangeRequestHandler, directory=args.root) - webbrowser.open(f"https://{args.bind}:{args.port}") + webbrowser.open(f"http://{args.bind}:{args.port}") with ThreadedTCPServer((args.bind, args.port), handler) as httpd: print( - f"Serving HTTPS on {args.bind} port {args.port} (https://{args.bind}:{args.port}/)" + f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)" ) httpd.serve_forever() |
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| diff -r 7e867ff86e44 -r f350467f9433 jbrowse2.py --- a/jbrowse2.py Thu Mar 07 00:27:48 2024 +0000 +++ b/jbrowse2.py Thu Mar 07 04:51:43 2024 +0000 |
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| b'@@ -602,23 +602,17 @@\n useuri = trackData["useuri"].lower() == "yes"\n if useuri:\n uri = data\n- adapt = {\n- "type": "HicAdapter",\n- "hicLocation": uri,\n- "locationType": "UriLocation",\n- },\n else:\n uri = trackData["hic_url"]\n- adapt = {\n- "type": "HicAdapter",\n- "hicLocation": uri,\n- },\n trackDict = {\n "type": "HicTrack",\n "trackId": tId,\n "name": uri,\n "assemblyNames": [self.genome_name],\n- "adapter": adapt,\n+ "adapter": {\n+ "type": "HicAdapter",\n+ "hicLocation": uri,\n+ },\n "displays": [\n {\n "type": "LinearHicDisplay",\n@@ -787,21 +781,13 @@\n useuri = trackData["useuri"].lower() == "yes"\n if useuri:\n url = data\n- adapt = {\n- "type": "BigWigAdapter",\n- "bigWigLocation": {"uri": url},\n- "locationType": "UriLocation",\n- }\n else:\n url = "%s.bigwig" % trackData["label"]\n # slashes in names cause path trouble\n dest = os.path.join(self.outdir, url)\n cmd = ["cp", data, dest]\n self.subprocess_check_call(cmd)\n- adapt = {\n- "type": "BigWigAdapter",\n- "bigWigLocation": {"uri": url},\n- }\n+ bwloc = {"uri": url}\n tId = trackData["label"]\n trackDict = {\n "type": "QuantitativeTrack",\n@@ -810,7 +796,10 @@\n "assemblyNames": [\n self.genome_name,\n ],\n- "adapter": adapt,\n+ "adapter": {\n+ "type": "BigWigAdapter",\n+ "bigWigLocation": bwloc,\n+ },\n "displays": [\n {\n "type": "LinearWiggleDisplay",\n@@ -829,31 +818,12 @@\n bindex = bam_index\n if useuri:\n url = data\n- adapt = {\n- "type": "BamAdapter",\n- "bamLocation": {"uri": url},\n- "index": {\n- "location": {\n- "uri": bindex,\n- "locationType": "UriLocation",\n- }\n- }\n- }\n else:\n fname = "%s.bam" % trackData["label"]\n dest = "%s/%s" % (self.outdir, fname)\n url = fname\n bindex = fname + \'.bai\'\n self.subprocess_check_call(["cp", data, dest])\n- adapt = {\n- "type": "BamAdapter",\n- "bamLocation": {"uri": url},\n- "index": {\n- "location": {\n- "uri": bindex,\n- }\n- }\n- }\n if bam_index is not None and os.path.exists(bam_index):\n if not os.path.exists(bindex):\n # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest\n@@ -874,7 +844,15 @@\n "trackId": tId,\n "name": trackData["name"],\n "assemblyNames": [self.genome_name],\n- "adapter": adapt,\n+ "adapter": {\n+ "type": "BamAdapter",\n+ "bamLocation": {"uri": url},\n+ "index": {\n+ "location": {\n+ "uri": bindex,\n+ }\n+ },\n+ },\n "displays": [\n {\n "type": "LinearAlignmentsDisplay",\n@@ -893,29 +871,13 @@\n bindex = cram_index\n if useuri:\n url = data\n- adapt = {\n- "type": "CramAdapter",\n- "cramLocation": {"uri": url},\n- "craiLocation": {\n- '..b' "uri": url\n@@ -991,13 +952,7 @@\n "uri": url + ".tbi",\n }\n },\n- }\n- trackDict = {\n- "type": "VariantTrack",\n- "trackId": tId,\n- "name": trackData["name"],\n- "assemblyNames": [self.genome_name],\n- "adapter": adapt,\n+ },\n "displays": [\n {\n "type": "LinearVariantDisplay",\n@@ -1040,24 +995,17 @@\n useuri = trackData["useuri"].lower() == "yes"\n if useuri:\n url = trackData["path"]\n- adapter = {\n- "type": "Gff3TabixAdapter",\n- "gffGzLocation": {\n- "uri": url,\n- "locationType": "UriLocation",\n- },\n- "index": {\n- "location": {\n- "uri": url + ".tbi",\n- "locationType": "UriLocation",\n- }\n- },\n- }\n else:\n url = "%s.%s.gz" % (trackData["label"], ext)\n dest = "%s/%s" % (self.outdir, url)\n self._sort_gff(data, dest)\n- adapter = {\n+ tId = trackData["label"]\n+ trackDict = {\n+ "type": "FeatureTrack",\n+ "trackId": tId,\n+ "name": trackData["name"],\n+ "assemblyNames": [self.genome_name],\n+ "adapter": {\n "type": "Gff3TabixAdapter",\n "gffGzLocation": {\n "uri": url,\n@@ -1067,14 +1015,7 @@\n "uri": url + ".tbi",\n }\n },\n- }\n- tId = trackData["label"]\n- trackDict = {\n- "type": "FeatureTrack",\n- "trackId": tId,\n- "name": trackData["name"],\n- "assemblyNames": [self.genome_name],\n- "adapter": adapt,\n+ },\n "displays": [\n {\n "type": "LinearBasicDisplay",\n@@ -1096,24 +1037,16 @@\n useuri = trackData["useuri"].lower() == "yes"\n if useuri:\n url = data\n- adapt = {\n- "type": "BedTabixAdapter",\n- "bedGzLocation": {\n- "uri": url,\n- "locationType": "UriLocation",\n- },\n- "index": {\n- "location": {\n- "uri": url + ".tbi",\n- "locationType": "UriLocation",\n- }\n- },\n- }\n else:\n url = "%s.%s.gz" % (trackData["label"], ext)\n dest = "%s/%s" % (self.outdir, url)\n self._sort_bed(data, dest)\n- adapt = {\n+ trackDict = {\n+ "type": "FeatureTrack",\n+ "trackId": tId,\n+ "name": trackData["name"],\n+ "assemblyNames": [self.genome_name],\n+ "adapter": {\n "type": "BedTabixAdapter",\n "bedGzLocation": {\n "uri": url,\n@@ -1123,13 +1056,7 @@\n "uri": url + ".tbi",\n }\n },\n- }\n- trackDict = {\n- "type": "FeatureTrack",\n- "trackId": tId,\n- "name": trackData["name"],\n- "assemblyNames": [self.genome_name],\n- "adapter": adapt,\n+ },\n "displays": [\n {\n "type": "LinearBasicDisplay",\n@@ -1179,7 +1106,11 @@\n "trackId": tId,\n "assemblyNames": passnames,\n "name": tname,\n- "adapter": adapt,\n+ "adapter": {\n+ "type": "PAFAdapter",\n+ "pafLocation": {"uri": url},\n+ "assemblyNames": passnames,\n+ },\n # "displays": [\n # {\n # "type": "LinearSyntenyDisplay",\n' |
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| diff -r 7e867ff86e44 -r f350467f9433 klBraLanc5.haps_combined.decontam.20230620.fasta.fa.gz |
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| Binary file klBraLanc5.haps_combined.decontam.20230620.fasta.fa.gz has changed |
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| diff -r 7e867ff86e44 -r f350467f9433 more --- a/more Thu Mar 07 00:27:48 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,58 +0,0 @@ -jbrowse2.py:2:80: E501 line too long (94 > 79 characters) -jbrowse2.py:84:80: E501 line too long (124 > 79 characters) -jbrowse2.py:85:80: E501 line too long (83 > 79 characters) -jbrowse2.py:88:80: E501 line too long (83 > 79 characters) -jbrowse2.py:102:80: E501 line too long (86 > 79 characters) -jbrowse2.py:234:80: E501 line too long (87 > 79 characters) -jbrowse2.py:261:80: E501 line too long (84 > 79 characters) -jbrowse2.py:266:80: E501 line too long (84 > 79 characters) -jbrowse2.py:267:80: E501 line too long (85 > 79 characters) -jbrowse2.py:275:80: E501 line too long (85 > 79 characters) -jbrowse2.py:283:80: E501 line too long (85 > 79 characters) -jbrowse2.py:295:80: E501 line too long (84 > 79 characters) -jbrowse2.py:348:80: E501 line too long (87 > 79 characters) -jbrowse2.py:351:80: E501 line too long (83 > 79 characters) -jbrowse2.py:357:80: E501 line too long (107 > 79 characters) -jbrowse2.py:367:80: E501 line too long (118 > 79 characters) -jbrowse2.py:392:80: E501 line too long (82 > 79 characters) -jbrowse2.py:461:80: E501 line too long (80 > 79 characters) -jbrowse2.py:554:80: E501 line too long (101 > 79 characters) -jbrowse2.py:558:80: E501 line too long (90 > 79 characters) -jbrowse2.py:560:80: E501 line too long (94 > 79 characters) -jbrowse2.py:562:80: E501 line too long (94 > 79 characters) -jbrowse2.py:563:80: E501 line too long (123 > 79 characters) -jbrowse2.py:597:80: E501 line too long (133 > 79 characters) -jbrowse2.py:605:80: E501 line too long (124 > 79 characters) -jbrowse2.py:624:80: E501 line too long (87 > 79 characters) -jbrowse2.py:783:80: E501 line too long (81 > 79 characters) -jbrowse2.py:784:80: E501 line too long (97 > 79 characters) -jbrowse2.py:790:80: E501 line too long (102 > 79 characters) -jbrowse2.py:791:80: E501 line too long (101 > 79 characters) -jbrowse2.py:792:80: E501 line too long (99 > 79 characters) -jbrowse2.py:794:80: E501 line too long (84 > 79 characters) -jbrowse2.py:830:80: E501 line too long (83 > 79 characters) -jbrowse2.py:831:80: E501 line too long (93 > 79 characters) -jbrowse2.py:837:80: E501 line too long (102 > 79 characters) -jbrowse2.py:838:80: E501 line too long (101 > 79 characters) -jbrowse2.py:839:80: E501 line too long (99 > 79 characters) -jbrowse2.py:841:80: E501 line too long (86 > 79 characters) -jbrowse2.py:843:80: E501 line too long (81 > 79 characters) -jbrowse2.py:925:80: E501 line too long (82 > 79 characters) -jbrowse2.py:1126:80: E501 line too long (84 > 79 characters) -jbrowse2.py:1193:80: E501 line too long (81 > 79 characters) -jbrowse2.py:1206:80: E501 line too long (80 > 79 characters) -jbrowse2.py:1243:80: E501 line too long (146 > 79 characters) -jbrowse2.py:1245:80: E501 line too long (83 > 79 characters) -jbrowse2.py:1260:80: E501 line too long (123 > 79 characters) -jbrowse2.py:1295:80: E501 line too long (107 > 79 characters) -jbrowse2.py:1301:80: E501 line too long (106 > 79 characters) -jbrowse2.py:1309:80: E501 line too long (80 > 79 characters) -jbrowse2.py:1314:80: E501 line too long (87 > 79 characters) -jbrowse2.py:1347:80: E501 line too long (82 > 79 characters) -jbrowse2.py:1354:80: E501 line too long (80 > 79 characters) -jbrowse2.py:1408:80: E501 line too long (86 > 79 characters) -jbrowse2.py:1432:80: E501 line too long (117 > 79 characters) -jbrowse2.py:1494:80: E501 line too long (94 > 79 characters) -jbrowse2.py:1504:80: E501 line too long (88 > 79 characters) -jbrowse2.py:1517:80: E501 line too long (86 > 79 characters) -jbrowse2.py:1549:80: E501 line too long (80 > 79 characters) |
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| diff -r 7e867ff86e44 -r f350467f9433 readme.rst --- a/readme.rst Thu Mar 07 00:27:48 2024 +0000 +++ b/readme.rst Thu Mar 07 04:51:43 2024 +0000 |
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| @@ -2,9 +2,9 @@ ================== Added Mar 3: -- optional tracks at last for JB2 - - dotted noodles from optional inputs now ignored without harm -- autogenJB2. + - optional tracks at last for JB2 + - dotted noodles from optional inputs now ignored without harm + - autogenJB2. - Takes a collection of bam/vcf etc and turns them into tracks in a normal JB2 history item. - Uses the JbrowseConnector, but the XML tool drives it from the contents of the collection. - Collection can be built from any source or with optional noodles in a WF |