| Previous changeset 96:5ef1ba2031f2 (2024-04-25) Next changeset 98:b1260bca5fdc (2024-06-05) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99 |
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modified:
autogenJB2.py jbrowse2.py jbrowse2.xml macros.xml readme.rst |
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added:
README.md Screenshot at 2024-04-30 16-11-29.png dm4_in_jb2.png jb210demotracks.png jb2_samplerMay5.png jbrowse8.png |
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| diff -r 5ef1ba2031f2 -r 74074746ccd8 Screenshot at 2024-04-30 16-11-29.png |
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| diff -r 5ef1ba2031f2 -r 74074746ccd8 autogenJB2.py --- a/autogenJB2.py Thu Apr 25 07:25:52 2024 +0000 +++ b/autogenJB2.py Sat Jun 01 05:37:13 2024 +0000 |
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| @@ -77,7 +77,7 @@ for i, x in enumerate(genome_paths) ], ) - logging.debug("@@@ paths=%s, genomes=%s" % (genome_paths, genomes)) + logging.debug("@@@autogenJB2 paths=%s, genomes=%s" % (genome_paths, genomes)) assref_name = jc.process_genomes(genomes[0]) if not default_session_data.get(assref_name, None): default_session_data[assref_name] = { @@ -90,7 +90,6 @@ }, } listtracks = trackList - # foo.paf must have a foo_paf.fasta or fasta.gz to match tnames = [x[2] for x in listtracks] texts = [x[1] for x in listtracks] for i, track in enumerate(listtracks): @@ -105,22 +104,20 @@ if tpath.startswith("http://") or tpath.startswith("https://"): useuri = "yes" if trext == "paf": - refname = trackname + "_paf.fasta" - refdat = [x[2] for x in listtracks if x[2] == refname] - if not refdat: + refdat = ["%s ~ %s" % (x[0],x[2]) for x in listtracks if x[1] in ["fasta", "fasta.gz"]] + if len(refdat) == 0: jc.logging.warn( - "!! No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf" - % (refname, trackname) + "!! No reference file for %s found. Using main reference" + % (refname) ) - sys.exit(3) + refdat = ["%s ~ %s" % (genomes[0].path, assref_name),] else: track_conf.update( { "conf": { "options": { "paf": { - "genome": refdat, - "genome_label": trackname, + "genome": ",".join(refdat) } } } |
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| diff -r 5ef1ba2031f2 -r 74074746ccd8 jbrowse2.py --- a/jbrowse2.py Thu Apr 25 07:25:52 2024 +0000 +++ b/jbrowse2.py Sat Jun 01 05:37:13 2024 +0000 |
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| b'@@ -22,7 +22,7 @@\n JB2VER = "v2.11.0"\n # version pinned if cloning - but not cloning now\n logCommands = True\n-# useful for seeing what\'s being written but not for production setups\n+# useful for seeing what\'s being written but NOT for production setups\n TODAY = datetime.datetime.now().strftime("%Y-%m-%d")\n SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))\n GALAXY_INFRASTRUCTURE_URL = None\n@@ -41,32 +41,6 @@\n }\n \n \n-INDEX_TEMPLATE = """<!doctype html>\n-<html lang="en" style="height:100%">\n-<head>\n-<meta charset="utf-8"/>\n-<link rel="shortcut icon" href="./favicon.ico"/>\n-<meta name="viewport" content="width=device-width,initial-scale=1"/>\n-<meta name="theme-color" content="#000000"/>\n-<meta name="description" content="A fast and flexible genome browser"/>\n-<link rel="manifest" href="./manifest.json"/>\n-<title>JBrowse</title>\n-</script>\n-</head>\n-<body style="overscroll-behavior:none; height:100%; margin: 0;">\n-<iframe\n- id="jbframe"\n- title="JBrowse2"\n- frameborder="0"\n- width="100%"\n- height="100%"\n- src=\'index_noview.html?config=config.json__SESSION_SPEC__\'>\n-</iframe>\n-</body>\n-</html>\n-"""\n-\n-\n class ColorScaling(object):\n \n COLOR_FUNCTION_TEMPLATE = """\n@@ -491,7 +465,8 @@\n nrow = len(fl)\n else:\n try:\n- scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)\n+ scontext = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)\n+ scontext.check_hostname = False\n scontext.verify_mode = ssl.VerifyMode.CERT_NONE\n with urllib.request.urlopen(url, context=scontext) as f:\n fl = f.readlines()\n@@ -544,7 +519,8 @@\n """\n if useuri:\n faname = fapath\n- scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)\n+ scontext = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)\n+ scontext.check_hostname = False\n scontext.verify_mode = ssl.VerifyMode.CERT_NONE\n with urllib.request.urlopen(url=faname + ".fai", context=scontext) as f:\n fl = f.readline()\n@@ -897,7 +873,7 @@\n genseqad = gsa[0]["genome_sequence_adapter"]\n else:\n genseqad = "Not found"\n- logging.warn("No adapter found for cram %s in gsa=%s" % (tId, gsa))\n+ logging.warning("No adapter found for cram %s in gsa=%s" % (tId, gsa))\n if useuri:\n url = data\n else:\n@@ -965,7 +941,7 @@\n url = data\n else:\n url = tId\n- dest = "%s/%s" % (self.outdir, url)\n+ dest = os.path.join(self.outdir, url)\n cmd = "bgzip -c %s > %s" % (data, dest)\n self.subprocess_popen(cmd)\n cmd = ["tabix", "-f", "-p", "vcf", dest]\n@@ -1032,7 +1008,7 @@\n url = trackData["path"]\n else:\n url = tId + ".gz"\n- dest = "%s/%s" % (self.outdir, url)\n+ dest = os.path.join(self.outdir, url)\n self._sort_gff(data, dest)\n categ = trackData["category"]\n trackDict = {\n@@ -1078,7 +1054,7 @@\n url = data\n else:\n url = tId + ".gz"\n- dest = "%s/%s" % (self.outdir, url)\n+ dest = os.path.join(self.outdir, url)\n self._sort_bed(data, dest)\n trackDict = {\n "type": "FeatureTrack",\n@@ -1125,7 +1101,7 @@\n url = tId\n useuri = data.startswith("http://") or data.startswith("https://")\n if not useuri:\n- dest = "%s/%s" % (self.outdir, url)\n+ dest = os.path.join(self.outdir, url)\n self.symlink_or_copy(os.path.realpath(data), dest)\n nrow = self.getNrow(dest)\n else:\n@@ -1327,6 +1303,7 @@\n https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py\n """\n # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708\n+ bpPerPx = 50 '..b' % ddl\n )\n+ view_json = {\n+ "type": "LinearGenomeView",\n+ "offsetPx": 0,\n+ "bpPerPx" : bpPerPx,\n+ "minimized": False,\n+ "tracks": tracks_data\n+ }\n if drdict.get("refName", None):\n # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome\n view_json["displayedRegions"] = [\n@@ -1415,7 +1392,6 @@\n for key, value in mapped_chars.items():\n session_name = session_name.replace(value, key)\n session_json["name"] = session_name\n-\n if "views" not in session_json:\n session_json["views"] = session_views\n else:\n@@ -1429,14 +1405,7 @@\n \n def add_defsess_to_index(self, data):\n """\n- PROBABLY NOW BROKEN by changes since this was deprecated temporarily as at April 18\n-\n- Included on request of the new codeowner, from Anthony\'s IUC PR.\n- Had to be fixed to keep each assembly with the associated tracks for a default view.\n- Originally used only the first assembly, putting all tracks there and so breaking some\n- when tested with 2 or more.\n-\n- ----------------------------------------------------------\n+ ----------------------------------------------------------\n Add some default session settings: set some assemblies/tracks on/off\n \n This allows to select a default view:\n@@ -1461,6 +1430,33 @@\n https://github.com/GMOD/jbrowse-components/discussions/3568\n https://github.com/GMOD/jbrowse-components/pull/4148\n """\n+\n+\n+ INDEX_TEMPLATE = """<!doctype html>\n+ <html lang="en" style="height:100%">\n+ <head>\n+ <meta charset="utf-8"/>\n+ <link rel="shortcut icon" href="./favicon.ico"/>\n+ <meta name="viewport" content="width=device-width,initial-scale=1"/>\n+ <meta name="theme-color" content="#000000"/>\n+ <meta name="description" content="A fast and flexible genome browser"/>\n+ <link rel="manifest" href="./manifest.json"/>\n+ <title>JBrowse</title>\n+ </script>\n+ </head>\n+ <body style="overscroll-behavior:none; height:100%; margin: 0;">\n+ <iframe\n+ id="jbframe"\n+ title="JBrowse2"\n+ frameborder="0"\n+ width="100%"\n+ height="100%"\n+ src=\'index_noview.html?config=config.json__SESSION_SPEC__\'>\n+ </iframe>\n+ </body>\n+ </html>\n+ """\n+\n new_index = "Nothing written"\n session_spec = {"views": []}\n logging.debug("def ass_first=%s\\ndata=%s" % (self.ass_first_contigs, data))\n@@ -1544,10 +1540,15 @@\n "version.txt",\n "test_data",\n ]:\n- cmd = ["rm", "-rf", os.path.join(dest, fn)]\n- self.subprocess_check_call(cmd)\n- cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest]\n- self.subprocess_check_call(cmd)\n+ try:\n+ path = os.path.join(dest, fn)\n+ if os.path.isdir(path):\n+ shutil.rmtree(path)\n+ else:\n+ os.remove(path)\n+ except OSError as e:\n+ log.error("Error: %s - %s." % (e.filename, e.strerror))\n+ shutil.copyfile(os.path.join(INSTALLED_TO, "jb2_webserver.py"), os.path.join(dest, "jb2_webserver.py"))\n \n \n def parse_style_conf(item):\n@@ -1561,7 +1562,7 @@\n parser = argparse.ArgumentParser(description="", epilog="")\n parser.add_argument("--xml", help="Track Configuration")\n parser.add_argument(\n- "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda"\n+ "--jbrowse2path", help="Path to JBrowse2 directory in BioContainer or Conda"\n )\n parser.add_argument("--outdir", help="Output directory", default="out")\n parser.add_argument("--version", "-V", action="version", version=JB2VER)\n' |
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| diff -r 5ef1ba2031f2 -r 74074746ccd8 jbrowse2.xml --- a/jbrowse2.xml Thu Apr 25 07:25:52 2024 +0000 +++ b/jbrowse2.xml Sat Jun 01 05:37:13 2024 +0000 |
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| b'@@ -3,12 +3,23 @@\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="edamInc" />\n+ <expand macro="edamInc"/>\n <xrefs>\n <xref type="bio.tools">jbrowse2</xref>\n </xrefs>\n <expand macro="requirements" />\n+ <expand macro="creators"/>\n <version_command>python \'${__tool_directory__}/jbrowse2.py\' --version</version_command>\n+ <required_files>\n+ <include path="autogenJB2.py" />\n+ <include path="blastxml_to_gapped_gff3.py" />\n+ <include path="convertMAF.sh" />\n+ <include path="gff3_rebase.py" />\n+ <include path="jb2_urlconf.py" />\n+ <include path="jb2_webserver.py" />\n+ <include path="jbrowse2.py" />\n+ <include path="maf2bed.py" />\n+ </required_files>\n <command detect_errors="aggressive"><![CDATA[\n mkdir -p \'$output.files_path\' &&\n cp \'$trackxml\' \'$output.files_path/galaxy.xml\' &&\n@@ -19,9 +30,9 @@\n #if $autoCollection[$key].is_collection:\n #set subCol=$autoCollection[$key]\n #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == \'paf\']\n+ #set refs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext in [\'fasta.gz\',\'fasta\']]\n #if len($pafs) > 0:\n --pafmeta \'$pafs[0]\'\n- #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == \'fasta\']\n #for $ref in $refs:\n --pafreferencemeta \'$ref\'\n #end for\n@@ -310,67 +321,39 @@\n ]]></configfile>\n </configfiles>\n <inputs>\n- <repeat name="assemblies" min="1"\n- title="Genome reference to provide display coordinates for this set of tracks"\n- help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files">\n+ <repeat name="assemblies" min="1" title="Genome reference to provide display coordinates for this set of tracks" help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files">\n <conditional name="reference_genome">\n- <param help="Select a built in, history or remote tabix URI for the reference track"\n- label="Reference genome source" name="genome_type_select" type="select">\n+ <param name="genome_type_select" type="select" label="Reference genome source" help="Select a built in, history or remote tabix URI for the reference track">\n <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>\n <option value="history">Use a genome fasta file from the current history</option>\n <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as\n tabix bgzip with predictable index file URI</option>\n </param>\n <when value="indexed">\n- <param\n- help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome"\n- label="Select a built in reference genome or custom genome"\n- name="genome"\n- type="select"\n- optional="true">\n+ <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome">\n <options from_data_table="all_fasta">\n- <filter column="2" type="sort_by" />\n- <validator\n- message="No genomes are available for the selected input dataset"\n- type="no_options">\n+ <filter column="2" type="sort_by"/>\n+ <validator message="No genomes are available for the selec'..b'ion name="jbcolor_scale">\n <conditional name="color_score">\n- <param name="color_score_select" value="none" />\n+ <param name="color_score_select" value="none"/>\n </conditional>\n <conditional name="color">\n- <param name="color_select" value="automatic" />\n+ <param name="color_select" value="automatic"/>\n </conditional>\n </section>\n </conditional>\n </repeat>\n <repeat name="data_tracks">\n <conditional name="data_format">\n- <param name="data_format_select" value="gff" />\n+ <param name="data_format_select" value="gff"/>\n <conditional name="useuri">\n- <param name="annotation" value="gff3/2.gff" />\n- <param name="insource" value="history" />\n+ <param name="annotation" value="gff3/2.gff"/>\n+ <param name="insource" value="history"/>\n </conditional>\n <conditional name="match_part">\n- <param name="match_part_select" value="true" />\n- <param name="name" value="cDNA_match" />\n+ <param name="match_part_select" value="true"/>\n+ <param name="name" value="cDNA_match"/>\n </conditional>\n <section name="jbcolor_scale">\n <conditional name="color_score">\n- <param name="color_score_select" value="none" />\n+ <param name="color_score_select" value="none"/>\n </conditional>\n <conditional name="color">\n- <param name="color_select" value="automatic" />\n+ <param name="color_select" value="automatic"/>\n </conditional>\n </section>\n </conditional>\n </repeat>\n </repeat>\n </repeat>\n-\n- <param name="uglyTestingHack" value="enabled" />\n+ <param name="uglyTestingHack" value="enabled"/>\n <output name="output">\n <assert_contents>\n- <has_text text="Ignore Scale" />\n- <has_text text="A.gff" />\n- <has_text text="B.gff" />\n- <has_text text="C.gff" />\n- <has_text text="interpro.gff" />\n- <has_text text="Scaled Colour" />\n- <has_text text="1.gff" />\n- <has_text text="2.gff" />\n+ <has_text text="Ignore Scale"/>\n+ <has_text text="A.gff"/>\n+ <has_text text="B.gff"/>\n+ <has_text text="C.gff"/>\n+ <has_text text="interpro.gff"/>\n+ <has_text text="Scaled Colour"/>\n+ <has_text text="1.gff"/>\n+ <has_text text="2.gff"/>\n </assert_contents>\n </output>\n </test>\n-\n <!-- TODO add a synteny test -->\n <!-- TODO add a bam and a cram test -->\n <!-- TODO add an hic test -->\n@@ -1275,7 +1197,7 @@\n they should adjust feature locations by 3x.\n \n \n-@ATTRIBUTION@\n ]]></help>\n- <expand macro="citations" />\n-</tool>\n\\ No newline at end of file\n+ <expand macro="citations"/>\n+ <expand macro="creators"/>\n+</tool>\n' |
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| diff -r 5ef1ba2031f2 -r 74074746ccd8 macros.xml --- a/macros.xml Thu Apr 25 07:25:52 2024 +0000 +++ b/macros.xml Sat Jun 01 05:37:13 2024 +0000 |
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| b'@@ -1,7 +1,6 @@\n-<?xml version="1.0"?>\n <macros>\n <token name="@TOOL_VERSION@">2.11.0</token>\n- <xml name = "edamInc">\n+ <xml name="edamInc">\n <edam_topics>\n <edam_topic>topic_3307</edam_topic>\n <edam_topic>topic_0092</edam_topic>\n@@ -33,100 +32,65 @@\n maintained by Ross Lazarus and Bjoern Gruening until the IUC complete their own.\n ]]>\n </token>\n+ <xml name="creators">\n+ <creator>\n+ <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena" />\n+ <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud" />\n+ <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/" />\n+ </creator>\n+ </xml>\n <xml name="genome_selector"\n token_help=""\n token_label="Fasta sequences"\n token_optional="False" >\n <conditional name="reference_genome">\n- <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">\n+ <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references">\n <option selected="True" value="indexed">Use a built-in genome</option>\n <option value="history">Use a genome from history</option>\n </param>\n <when value="indexed">\n- <param\n- help="@HELP@"\n- label="@LABEL@"\n- name="genomes"\n- type="select"\n- optional="@OPTIONAL@"\n- >\n+ <param name="genomes" type="select" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@">\n <options from_data_table="all_fasta">\n- <filter column="2" type="sort_by" />\n- <validator message="No genomes are available for the selected input dataset" type="no_options" />\n+ <filter column="2" type="sort_by"/>\n+ <validator message="No genomes are available for the selected input dataset" type="no_options"/>\n </options>\n </param>\n </when>\n <when value="history">\n- <param\n- format="fasta"\n- label="@LABEL@"\n- help="@HELP@"\n- name="genomes"\n- type="data"\n- optional="@OPTIONAL@"\n- multiple="True" />\n+ <param name="genomes" type="data" format="fasta" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@" multiple="True"/>\n </when>\n </conditional>\n </xml>\n-\n- <xml name="auto_manual_tk"\n- token_cond_label="Color"\n- token_cond_name="color"\n- token_select_label="Color Specification"\n- token_select_name="color_select"\n- token_automatic_label="Automatically selected"\n- token_manual_label="Manual Color Selection">\n+ <xml name="auto_manual_tk" token_cond_label="Color" token_cond_name="color" token_select_label="Color Specification" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection">\n <conditional name="@COND_NAME@" label="@COND_LABEL@">\n- <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">\n+ <param name="@SELECT_NAME@" type="select" label="@SELECT_LABEL@">\n <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>\n <option value="manual">@MANUAL_LABEL@</option>\n </param>\n <when value="automatic">\n </when>\n <when value="manual">\n- <yield />\n+ <yield/>\n </when>\n </conditional>\n </xml>\n-\n- <xml name="jb_color"\n- token_label="JBrowse style.color"\n- token_name="style_color"\n- token_value="golden'..b' </param>\n <when value="history">\n- <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />\n+ <param name="annotation" type="data" format="@FORMAT@" optional="true" label="@LABEL@" multiple="True"/>\n </when>\n <when value="uri">\n- <param label="@LABEL@" name="annouri" type="text" />\n- <param label="Short name for track display" name="annoname" type="text" >\n+ <param name="annouri" type="text" label="@LABEL@"/>\n+ <param name="annoname" type="text" label="Short name for track display">\n <sanitizer invalid_char="_">\n- <valid initial="string.printable" >\n- <remove value="\'" />\n- </valid>\n+ <valid initial="string.printable">\n+ <remove value="\'"/>\n+ </valid>\n </sanitizer>\n </param>\n </when>\n@@ -562,24 +461,22 @@\n </xml>\n <xml name="pafref_conditional" token_label="Track Data" token_format="data">\n <conditional name="pafuseuri">\n- <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?"\n- help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">\n+ <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">\n <option value="history" selected="true">PAF reference comparison genome from a history file</option>\n <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>\n </param>\n <when value="history">\n- <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data"\n- help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" />\n+ <param name="annotation" type="data" format="@FORMAT@" label="@LABEL@" help="Add all PAF reference comparison genomes used to make the PAF" multiple="true"/>\n </when>\n <when value="uri">\n <repeat name="refuri" title="PAF reference comparison genome URI" min="1">\n- <param label="@LABEL@" name="annotation" type="text" />\n- <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space">\n- <sanitizer invalid_char="_">\n- <valid initial="string.printable" >\n- <remove value="\'" />\n- </valid>\n- </sanitizer>\n+ <param name="annotation" type="text" label="@LABEL@"/>\n+ <param name="annoname" type="text" label="Short name for this reference" help="Short names take less track space">\n+ <sanitizer invalid_char="_">\n+ <valid initial="string.printable">\n+ <remove value="\'"/>\n+ </valid>\n+ </sanitizer>\n </param>\n </repeat>\n </when>\n@@ -587,8 +484,8 @@\n </xml>\n <xml name="citations">\n <citations>\n- <citation type="doi">10.1186/s13059-016-0924-1</citation>\n- <citation type="doi">10.1101/gr.094607.109</citation>\n+ <citation type="doi">10.1186/s13059-016-0924-1</citation>\n+ <citation type="doi">10.1101/gr.094607.109</citation>\n </citations>\n </xml>\n </macros>\n' |
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| diff -r 5ef1ba2031f2 -r 74074746ccd8 readme.rst --- a/readme.rst Thu Apr 25 07:25:52 2024 +0000 +++ b/readme.rst Sat Jun 01 05:37:13 2024 +0000 |
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| @@ -1,5 +1,16 @@ JBrowse2 in Galaxy ================== + + +Added April 2024: +Multiple independent assembly/track sets in the same browser now working +Tests are now far more convincing using the zip outputs to check for files +Automated collection generation is really cool - TODO: need visibility for each track +maf and blastxml are working for test files at least - not yet properly tested. +cool/mcool are converted to hic +vcf, cram, bam, bed, gff, bigwig, hic, cool, blastxml, maf, paf tracks. + + Added Mar 26: Testing history added with tests of the 8 simple formats hic and paf need small tests but work with big ones... @@ -29,9 +40,9 @@ .. image:: dm4_in_jb2.png -Other tracks +Other samples -.. image:: jbrowse8.png +.. image:: jb2_samplerMay5.png JBrowse2 is a fast, embeddable genome browser built completely with JavaScript and HTML5 @@ -69,17 +80,17 @@ - 2.10.0+galaxy2 - - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0 - - was working well enough for VGP when previous PR discovered - - too late to backport all the fixes - - working default session and some other ideas copied instead. - - seems to work well with defaults. - - need to document and implement track settings by running the browser locally. - - works well enough to be useful in workflows such as TreeValGal. - - JB2 seems to set defaults wisely. - - not yet ideal for users who need fine grained track control. - - synteny (paf + reference) now working - - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out. +- UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0 +- was working well enough for VGP when previous PR discovered + - too late to backport all the fixes + - working default session and some other ideas copied instead. +- seems to work well with defaults. +- need to document and implement track settings by running the browser locally. +- works well enough to be useful in workflows such as TreeValGal. +- JB2 seems to set defaults wisely. +- not yet ideal for users who need fine grained track control. +- synteny (paf + reference) now working +- rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out. Wrapper License (MIT/BSD Style) |
