From 4b09027ebbad5058af4aa882ae6b2fe520c386f9 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 15 Feb 2018 10:50:48 -0500
Subject: [PATCH] Update all tools/converters using UCSC binaries to depend
 only on the binary they are using.

---
 .../converters/bam_to_bigwig_converter.xml    |  2 +-
 .../bed_gff_or_vcf_to_bigwig_converter.xml    |  2 +-
 .../bedgraph_to_bigwig_converter.xml          |  2 +-
 .../datatypes/converters/fasta_to_2bit.xml    |  3 +-
 .../interval_to_bigwig_converter.xml          |  2 +-
 .../converters/sam_to_bigwig_converter.xml    |  2 +-
 .../converters/wig_to_bigwig_converter.xml    |  2 +-
 .../deps/resolvers/default_conda_mapping.yml  | 46 ++++++++++++++++++-
 tools/evolution/codingSnps.xml                |  3 +-
 tools/extract/extract_genomic_dna.xml         |  3 +-
 tools/extract/liftOver_wrapper.xml            |  2 +-
 tools/filters/bed_to_bigbed.xml               |  2 +-
 tools/filters/wig_to_bigwig.xml               |  2 +-
 13 files changed, 57 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
index 50b8c1ca14c..79a5452ed6a 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.0" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package">ucsc_tools</requirement>
+        <requirement type="package">ucsc-bedgraphtobigwig</requirement>
         <requirement type="package">bedtools</requirement>
     </requirements>
     <command><![CDATA[
diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
index 3a2c28cf6fa..27d9a2d46ac 100644
--- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.0" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package">ucsc_tools</requirement>
+        <requirement type="package">ucsc-bedgraphtobigwig</requirement>
         <requirement type="package">bedtools</requirement>
     </requirements>
     <command>
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
index 09c2da2d1a5..cc685d1164b 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.0" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
-        <requirement type="package">ucsc_tools</requirement>
+        <requirement type="package">ucsc-wigtobigwig</requirement>
     </requirements>
     <command>grep -v "^track" '$input' | wigToBigWig -clip stdin '$chromInfo' '$output'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
index 3ccd7ab7db8..d3574c97639 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
@@ -2,8 +2,7 @@
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
     <requirements>
-        <requirement type="package" version="332">ucsc-fatotwobit</requirement>
-        <requirement type="package">ucsc_tools</requirement>
+        <requirement type="package">ucsc-fatotwobit</requirement>
     </requirements>
     <command>faToTwoBit '$input' '$output'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
index c1231de7a55..35a495c3e68 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.0">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package">ucsc_tools</requirement>
+        <requirement type="package">ucsc-bedgraphtobigwig</requirement>
         <requirement type="package">bedtools</requirement>
     </requirements>
     <command>
diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
index 93fc18d2abe..44373907bbe 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true">
     <requirements>
-        <requirement type="package">ucsc_tools</requirement>
+        <requirement type="package">ucsc-bedgraphtobigwig</requirement>
         <requirement type="package">samtools</requirement>
         <requirement type="package">bedtools</requirement>
     </requirements>
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index 3f972c96545..871c712c385 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.0" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
-        <requirement type="package">ucsc_tools</requirement>
+        <requirement type="package">ucsc-wigtobigwig</requirement>
     </requirements>
     <command>
 <![CDATA[
diff --git a/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml b/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
index 273fb5020e8..3c0663d3e84 100644
--- a/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
+++ b/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
@@ -13,7 +13,7 @@
     unversioned: true
   to:
     name: ucsc_tools
-    version: 332
+    version: 357
 - from:
     name: bedtools
     unversioned: true
@@ -44,4 +44,46 @@
   to:
     name: bowtie
     version: 1.2.0
-  
\ No newline at end of file
+- from:
+    name: ucsc-bedgraphtobigwig
+    unversioned: true
+  to:
+    name: ucsc-bedgraphtobigwig
+    version: 357
+- from:
+    name: ucsc-bedtobigbed
+    unversioned: true
+  to:
+    name: ucsc-bedtobigbed
+    version: 357
+- from:
+    name: ucsc-fatotwobit
+    unversioned: true
+  to:
+    name: ucsc-fatotwobit
+    version: 357
+- from:
+    name: ucsc-liftover
+    unversioned: true
+  to:
+    name: ucsc-liftover
+    version: 357
+- from:
+    name: ucsc-nibfrag
+    unversioned: true
+  to:
+    name: ucsc-nibfrag
+    version: 357
+- from:
+    name: ucsc-twobittofa
+    unversioned: true
+  to:
+    name: ucsc-twobittofa
+    version: 357
+- from:
+    name: ucsc-wigtobigwig
+    unversioned: true
+  to:
+    name: ucsc-wigtobigwig
+    version: 357
+
diff --git a/tools/evolution/codingSnps.xml b/tools/evolution/codingSnps.xml
index 345a9932ef9..1e97e9d7419 100644
--- a/tools/evolution/codingSnps.xml
+++ b/tools/evolution/codingSnps.xml
@@ -47,7 +47,8 @@
 
   <requirements>
     <requirement type="package">gnu_coreutils</requirement>
-    <requirement type="package">ucsc_tools</requirement>
+    <requirement type="package">ucsc-twobittofa</requirement>
+    <requirement type="package">ucsc-nibfrag</requirement>
   </requirements>
 
   <tests>
diff --git a/tools/extract/extract_genomic_dna.xml b/tools/extract/extract_genomic_dna.xml
index be20de23481..a0b5763511e 100644
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -1,8 +1,7 @@
 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.3">
   <description>using coordinates from assembled/unassembled genomes</description>
   <requirements>
-      <requirement type="package">ucsc_tools</requirement>
-      <requirement type="binary">faToTwoBit</requirement>
+      <requirement type="package">ucsc-fatotwobit</requirement>
   </requirements>
   <command>
       python '$__tool_directory__/extract_genomic_dna.py' '${input}' '${out_file1}' -o ${out_format} -d '${dbkey}'
diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
index ebf634ec234..00e4452d49d 100644
--- a/tools/extract/liftOver_wrapper.xml
+++ b/tools/extract/liftOver_wrapper.xml
@@ -1,7 +1,7 @@
 <tool id="liftOver1" name="Convert genome coordinates" version="1.0.5">
   <description> between assemblies and genomes</description>
   <requirements>
-    <requirement type="package">ucsc_tools</requirement>
+    <requirement type="package">ucsc-liftover</requirement>
   </requirements>
   <command>
   python $__tool_directory__/liftOver_wrapper.py
diff --git a/tools/filters/bed_to_bigbed.xml b/tools/filters/bed_to_bigbed.xml
index d72858ab7f4..68f8e68dbc4 100644
--- a/tools/filters/bed_to_bigbed.xml
+++ b/tools/filters/bed_to_bigbed.xml
@@ -10,7 +10,7 @@
     2&gt;&amp;1 || echo "Error running bedToBigBed." >&amp;2
   </command>
   <requirements>
-    <requirement type="package">ucsc_tools</requirement>
+    <requirement type="package">ucsc-bedtobigbed</requirement>
   </requirements>
   <inputs>
     <param format="bed" name="input1" type="data" label="Convert">
diff --git a/tools/filters/wig_to_bigwig.xml b/tools/filters/wig_to_bigwig.xml
index 261229dbdbb..46ef7cc9b88 100644
--- a/tools/filters/wig_to_bigwig.xml
+++ b/tools/filters/wig_to_bigwig.xml
@@ -1,7 +1,7 @@
 <tool id="wig_to_bigWig" name="Wig/BedGraph-to-bigWig" version="1.1.0">
   <description>converter</description>
   <requirements>
-    <requirement type="package">ucsc_tools</requirement>
+    <requirement type="package">ucsc-wigtobigwig</requirement>
   </requirements>
   <stdio>
       <!-- Anything other than zero is an error -->