Trackhubs

INSTALL.sh

@@ -30,6 +30,23 @@ fi
 sed -i 's#^FILE_PREFIX.*$#FILE_PREFIX = "/var/www"#' plotter/db.py
 sudo python setup.py install
 
+if [ "$TRAVIS" = "true" ]; then
+    cd $TRAVIS_BUILD_DIR
+else
+    cd
+fi
+mkdir kent
+cd kent
+if [ uname != "Darwin" ]; then
+    rsync -a -P rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedToBigBed ./
+    rsync -a -P rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig ./
+else
+    rsync -a -P rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.x86_64/bedToBigBed ./
+    rsync -a -P rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.x86_64/bedGraphToBigWig ./
+fi
+sudo cp bedToBigBed /usr/local/bin/
+sudo cp bedGraphToBigWig /usr/local/bin/
+
 # for an apache web server
 sudo apt-get install apache2 libapache2-mod-wsgi
 cd /var/www

plotter/__init__.py

@@ -29,6 +29,10 @@ def main(global_config, **settings):
     config.add_route('add_region',
               '/add_region/{name}/{chr}/{trackType}/{annotation}/{min}/{max}/')
     config.add_route("export","/export/{user}/{name}/{what}/{format}/")
+    config.add_route('trackhub_export', '/trackhub_init/{user}/')
+    config.add_route('trackhub_details', '/trackhub_details/{short_name}/')
+    config.add_route('trackhub_file', '/trackhub/{short_name}/*file')
+    config.add_route('trackhub_list', '/trackhub_list/{user}/')
     name_regex = db.HEADER_PATTERNS["name"]
     # config.add_route("secret","/secret/{name:%s}{suffix}"%name_regex)
     config.add_route("secret","/secret/{profile_name}/{name:%s}{suffix}"%name_regex)

plotter/db.py

@@ -855,6 +855,20 @@ def process(self):
         # print time.time()-before, "seconds elapsed"
 
 
+class Trackhub(Resource):
+    keys = ("short_name",)
+
+    def make_details(self):
+        return {}
+
+
+class UserTrackhubs(Resource):
+    keys = ("trackhubs",)
+
+    def make_details(self):
+        return []
+
+
 class Models(Resource):
     keys = ("name", "chr")
 

plotter/templates/export_table.pt

@@ -0,0 +1,42 @@
+<table class="home">
+  <tr>
+    <th>db</th>
+    <th>Uploaded by</th>
+    <th>on</th>
+    <th>Probes</th>
+    <th>Copy#</th>
+    <th>Bkpt</th>
+    <th colspan="2" >Annotations</th>
+    <th colspan="3" >Segmentation</th>
+    <th colspan="2" >Breakpoints</th>
+    <th colspan="1" >Links</th>
+  </tr>
+
+  <tr tal:repeat="p profiles" tal:switch="p.ready">
+    <td class="left" tal:condition="p.ready">
+      <input type="checkbox" name="profile" value="${p.name}">
+        ${p.name}
+      </input>
+    </td>
+    <td tal:condition="p.ready == False">
+      ${p.name}
+    </td>
+    <td>${p.db}</td>
+    <td tal:condition="str(user) == p.uploader">
+      you [<a href="/delete_profile/${p.name}/">Delete</a>]
+    </td>
+    <td tal:condition="str(user) != p.uploader">
+      ${p.uploader}
+    </td>
+    <td class="mono">${p.uploaded_on.strftime("%d-%b-%Y")}</td>
+    <td>${p.share}</td>
+    <td class="numeric">${p.probes}</td>
+    <td tal:condition="p.ready" class="numeric">
+      <div tal:condition="p.copies">${p.copies}</div>
+    </td>
+    <td tal:condition="p.ready" class="numeric">
+      <div tal:condition="p.breakpoints">${p.breakpoints}</div>
+    </td>
+  </tr>
+</table>
+

plotter/templates/profile_table.pt

@@ -3,9 +3,18 @@ If the profile name link is not active for a recently-uploaded profile,
 you need to wait a few minutes for the server to process the
 data. </p>
 
+  <form method="get" action="/trackhub_list/${user}/">
+    <button type="submit">View Your Track Hubs</button>
+</form>
+
+<form method="get" action="/trackhub_init/${user}/">
+    <button type="submit">Create Track Hub</button>
+</form>
+
 <form action="/view_profiles/" method="post"
       enctype="multipart/form-data">
 
+
 <table class="home">
   <tr>
     <th><input type="submit" value="Plot checked" /></th>

plotter/templates/trackhub_details.pt

@@ -0,0 +1,35 @@
+
+<metal:main use-macro="load: base.pt">
+  <title metal:fill-slot="title">
+    SegAnnDB: Trackhub Details
+  </title>
+
+  <div metal:fill-slot="content">
+
+      <p>
+          <br/>
+      Trackhub data for ${short_name}
+      </p>
+      <br/>
+      <p>
+          Description: ${long_name}
+      </p>
+      <br/>
+      <p>
+          URL: <a href="${url}">${url}</a>
+          <br/>
+          Paste this into UCSC's My Hub page to view your trackhub.
+      </p>
+      <br/>
+      <p>
+      Profiles:
+      <br/>
+      <div tal:repeat="p profiles">
+        <td>
+            <a href="/profile/${p}/">${p}</a>
+        </td>
+      </div>
+      <br/>
+<p>Return to <a href="/">home</a>.</p>
+  </div>
+</metal:main>

plotter/templates/trackhub_export.pt

@@ -0,0 +1,26 @@
+
+<metal:main use-macro="load: base.pt">
+  <title metal:fill-slot="title">>
+    SegAnnDB: Export Trackhub
+  </title>
+
+  <div metal:fill-slot="content">
+      <p>Please fill out the profile data.</p>
+      <form enctype="multipart/form-data" method="post">
+	<p><label for="id_short_label">Short Label:</label>
+        <input type="text" name="short_label" id="id_short_label" />
+        <label for="id_long_label">Long Label:</label>
+        <input type="text" name="long_label" id="id_long_label" />
+        <label for="id_db">DB</label>
+        <input type="text" name="db" id="id_db" />
+
+	</p>
+          <metal:main use-macro="load: export_table.pt"/>
+	 <input id="submit_button" type="submit"
+		value="Create Track Hub" />
+      </form>
+
+      <p>Return to <a href="/">home</a>.</p>
+
+  </div>
+</metal:main>

plotter/templates/trackhub_list.pt

@@ -0,0 +1,17 @@
+
+
+  <title>
+    SegAnnDB: Trackhub List for ${user}
+  </title>
+
+
+      <p>
+      Trackhubs:
+      </p>
+      <p>
+      <div tal:repeat="t trackhubs">
+        <td>
+        <a href="${url}/trackhub_details/${t}/">${t}</a>
+        </td>
+      </div>
+  </p>