Added BLAST, changed Login window

mictadlo · Feb 12, 2021 · 554d870 · 554d870
1 parent c185056
commit 554d870
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Showing 4 changed files with 33 additions and 2 deletions.
diff --git a/Apollo-2.6.2/Dockerfile b/Apollo-2.6.2/Dockerfile
@@ -15,7 +15,7 @@ RUN apt-get -qq update --fix-missing && \
 	apt-get --no-install-recommends -y install \
 	git locales locales-all build-essential libpq-dev wget python3-pip \
 	lsb-release gnupg2 wget xmlstarlet netcat libpng-dev postgresql-common \
-	zlib1g-dev libexpat1-dev curl ssl-cert zip unzip openjdk-8-jdk-headless
+	zlib1g-dev libexpat1-dev curl ssl-cert zip unzip openjdk-8-jdk-headless ncbi-blast+
 
 RUN sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list' && \
     wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
@@ -72,7 +72,7 @@ ENV LANGUAGE=en_US.UTF-8
 
 RUN pip3 install setuptools
 RUN pip3 install wheel
-RUN pip3 install nose apollo==4.2.7
+RUN pip3 install nose apollo==4.2.10
 
 RUN curl -s get.sdkman.io | bash && \
      /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install grails 2.5.5" && \

diff --git a/Apollo-2.6.2/docker-files/docker-apollo-config.groovy b/Apollo-2.6.2/docker-files/docker-apollo-config.groovy
@@ -139,6 +139,23 @@ apollo {
             "active": checkBooleanEnvironment("WEBAPOLLO_USER_PASSWORD_AUTH",true)
         ]
     ]
+    sequence_search_tools   {
+      blat_nuc      {
+         search_exe = "/usr/bin/blastn"
+         search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
+         name = "Blast nucleotide"
+         params = "-num_threads 2"
+         //tmp_dir = "/efs/apollo/tmp"
+
+      }
+      blat_prot      {
+          search_exe = "/usr/bin/tblastn"
+          search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
+          name = "Blast protein to translated nucleotide"
+          params = "-num_threads 2"
+          //tmp_dir = "/efs/apollo/tmp"
+      }
+   }
 }
 
 jbrowse {

diff --git a/Apollo-2.6.2/grails-app/views/auth/login.gsp b/Apollo-2.6.2/grails-app/views/auth/login.gsp
@@ -10,6 +10,13 @@
         <div class="message">${flash.message}</div>
     </g:if>
     <g:form action="signIn">
+        <br/>
+        <hr/>
+        <b>Access Disclaimer</b>: As a public service...
+        <br>
+            For Public access, please use <b>username:</b> anonymous@apollo.au  and  <b>password</b>: anonymous
+        <br/>
+        <br/>
         <input type="hidden" name="targetUri" value="${targetUri}" class="col-md-4"/>
         <div class="col-md-5 col-lg-offset-1" style="margin-top: 10px;">
             <input name="username" value="${username}" type="username" class="form-control col-md-4"

diff --git a/Apollo-2.6.2/src/gwt/org/bbop/apollo/gwt/client/LoginDialog.ui.xml b/Apollo-2.6.2/src/gwt/org/bbop/apollo/gwt/client/LoginDialog.ui.xml
@@ -34,6 +34,13 @@
         <b:Column size="MD_2"><b:Button ui:field="loginButton" type="PRIMARY">Login</b:Button></b:Column>
       </b:Row>
     </b:Container>
+
+    <b:Row styleName="{style.spacer}">
+          <gwt:HTML styleName="{style.inline-html}">
+               <h4>Access Disclaimer:</h4> As a public service ...
+               For Public access, please use <b>username:</b> anonymous@apollo.au  and  <b>password</b>: anonymous
+          </gwt:HTML>
+    </b:Row>
 
     <b:Row styleName="{style.spacer}">
       <b:Anchor text="Browse public genomes" href="../jbrowse/"/>