Mercurial > repos > gga > chado_phylogeny_gene_families

changeset 11:cb4cee85202a draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
author gga
date Mon, 08 Jul 2019 05:37:56 -0400
parents f8d27e79e363
children b9fd06875714
files macros.xml phylogeny_gene_families.xml prepare_psql.sh
diffstat 3 files changed, 97 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Mar 05 05:16:37 2019 -0500
+++ b/macros.xml	Mon Jul 08 05:37:56 2019 -0400
@@ -2,12 +2,16 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.2.5">python-chado</requirement>
+            <requirement type="package" version="2.2.6">python-chado</requirement>
             <requirement type="package" version="1.5">jq</requirement>
+            <requirement type="package" version="@PG_VERSION@">postgresql</requirement>
+            <requirement type="package" version="0.1">pglite</requirement>
             <yield/>
         </requirements>
     </xml>
 
+    <token name="@PG_VERSION@">11.2</token>
+
     <xml name="stdio">
         <stdio>
             <regex level="fatal" match="Exception:" source="stderr" />
@@ -16,7 +20,7 @@
         </stdio>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">2.2.5</token>
+    <token name="@WRAPPER_VERSION@">2.2.6</token>
 
     <xml name="citation">
         <citations>
@@ -32,19 +36,6 @@
     <token name="@HELP@"><![CDATA[
     ]]></token>
 
-    <token name="@AUTH@"><![CDATA[
-        echo "__default: local" > '.auth.yml' &&
-        echo "local:" >> '.auth.yml' &&
-        echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
-        echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
-        echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
-        echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
-        echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
-        echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
-
-        CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
-    ]]></token>
-
     <xml name="sanitized">
         <sanitizer>
             <valid initial="string.printable">
@@ -83,4 +74,63 @@
                label="Sequence type of the parent"
                help="this should be a Sequence Ontology term" />
     </xml>
+
+    <xml name="psql_target">
+      <conditional name="psql_target">
+         <param name="method" type="select" label="Chado Database" help="If you select 'Remote database' make sure credentials are defined in environment variables">
+              <option value="remote">Remote database</option>
+              <option value="pgtools">Database from history</option>
+          </param>
+          <when value="remote"/>
+          <when value="pgtools">
+            <param name="infile" type="data" format="postgresql" label="Input database" />
+            <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/>
+          </when>
+      </conditional>
+    </xml>
+
+    <token name="@AUTH@"><![CDATA[
+        if [ -z "$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
+          echo "__default: local" > '.auth.yml' &&
+          echo "local:" >> '.auth.yml' &&
+          echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
+          echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
+          echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
+          echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
+          echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
+          echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
+
+          export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
+        ; fi
+    ]]></token>
+
+    <token name="@START_PSQL@"><![CDATA[
+        #if $psql_target.method == 'pgtools'
+            tar -xjvf '$psql_target.infile' > /dev/null &&
+            . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
+        #else
+            @AUTH@
+        #end if
+    ]]></token>
+
+    <token name="@STOP_PSQL@"><![CDATA[
+        #if $psql_target.method == 'pgtools'
+            pglite stop -d ./postgresql &&
+            timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
+            ;
+            ## Make sure psql is stopped even if loading script failed
+            pglite stop -d ./postgresql || true
+        #end if
+    ]]></token>
+
+    <token name="@ZIP_PSQL@"><![CDATA[
+        #if $psql_target.method == 'pgtools'
+            pglite stop -d ./postgresql &&
+            timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' &&
+            tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null
+            ;
+            ## Make sure psql is stopped even if loading script failed
+            pglite stop -d ./postgresql || true
+        #end if
+    ]]></token>
 </macros>
--- a/phylogeny_gene_families.xml	Tue Mar 05 05:16:37 2019 -0500
+++ b/phylogeny_gene_families.xml	Mon Jul 08 05:37:56 2019 -0400
@@ -6,7 +6,7 @@
 	</macros>
 	<expand macro="requirements"/>
 	<command detect_errors="aggressive"><![CDATA[
-@AUTH@
+@START_PSQL@ &&
 
 chakin phylogeny gene_families
 
@@ -17,16 +17,22 @@
 $nuke
 
  > '$results'
+
+ && @ZIP_PSQL@
     ]]></command>
 	<inputs>
-        <!-- options -->
+		  <expand macro="psql_target"/>
+      <!-- options -->
     	<param name="family_name" label="Family Name" argument="--family_name" type="text" help="Restrict to families beginning with given prefix" />
     	<param name="nuke" label="Nuke" argument="--nuke" type="boolean" truevalue="--nuke" falsevalue="" help="Removes all previous gene families data" />
         <expand macro="wait_for"/>
 
 	</inputs>
 	<outputs>
-		<data format="txt" name="results"/>
+			<data format="txt" name="results"/>
+		  <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
+				<filter>psql_target['method'] == "pgtools"</filter>
+			</data>
 	</outputs>
 	<help>
 Adds an entry in the featureprop table in a chado database for each family a gene belongs to (for use in https://github.com/legumeinfo/lis_context_viewer/).
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prepare_psql.sh	Mon Jul 08 05:37:56 2019 -0400
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+export PWD=`pwd` &&
+sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '$PWD/postgresql/'|" ./postgresql/db/postgresql.conf &&
+
+pglite start  -d ./postgresql &&
+
+timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "server is running"; do sleep 1; done' &&
+pglite status -d ./postgresql &&
+timeout 60 bash -c 'until ls -la ./postgresql | grep -F -q ".s.PGSQL.5432"; do sleep 1; done' &&
+pglite status -d ./postgresql &&
+
+echo "__default: local" > '.auth.yml' &&
+echo "local:" >> '.auth.yml' &&
+echo "    dbhost: \"xxx\"" >> '.auth.yml' &&
+echo "    dbname: \"xxx\"" >> '.auth.yml' &&
+echo "    dbpass: \"xxx\"" >> '.auth.yml' &&
+echo "    dbuser: \"xxx\"" >> '.auth.yml' &&
+echo "    dbschema: \"$1\"" >> '.auth.yml' &&
+echo "    dbport: \"xxx\"" >> '.auth.yml' &&
+echo "    dburl: \"$(pglite url -d ./postgresql)\"" >> '.auth.yml' &&
+
+export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'