From cd7a2c3418d6540ab3bb3177b0b0216c54ebff56 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 13 Feb 2020 16:04:24 +0100
Subject: [PATCH] Bump bx-python to 0.8.8

---
 .../datatypes/converters/bed_to_interval_index_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml | 2 +-
 lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/interval_to_bed_converter.xml   | 2 +-
 .../datatypes/converters/interval_to_bedstrict_converter.xml    | 2 +-
 .../converters/interval_to_interval_index_converter.xml         | 2 +-
 .../datatypes/converters/pileup_to_interval_index_converter.xml | 2 +-
 .../datatypes/converters/vcf_to_interval_index_converter.xml    | 2 +-
 .../dependencies/pipfiles/default/pinned-requirements.txt       | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
index 60a06dc7753..98618ef4c68 100644
--- a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bed_to_interval_index_0" name="Convert BED to Interval Index" version="1.0.0" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_interval_index_converter.py' '$input1' '$output1'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
index e98a8f46d7d..ace96313d74 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed12_0" name="Convert Genomic Intervals To Strict BED12" version="1.0.0" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/interval_to_bedstrict_converter.py'
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
index f28f2a0f754..77f39d8dfa9 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed6_0" name="Convert Genomic Intervals To Strict BED6" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 6</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
index 4883b5e3dab..5ff627e8174 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED" version="1.0.0" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bed_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol}</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
index 07a4f140167..33203ae06d6 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bedstrict_0" name="Convert Genomic Intervals To Strict BED" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension}</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
index aaecd8ca53f..9c8d1a949c4 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_interval_index_0" name="Convert Interval to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/interval_to_interval_index_converter.py'
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
index 7f33398966f..7b960385095 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_pileup_to_interval_index_0" name="Convert Pileup to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/pileup_to_interval_index_converter.py'
diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
index 627b297c328..9c2c96fa559 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_vcf_to_interval_index_0" name="Convert VCF to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description>
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
         <requirement type="package" version="1.1.4">galaxy_sequence_utils</requirement>
     </requirements>
     <command>python '$__tool_directory__/vcf_to_interval_index_converter.py' '$input1' '$output1'</command>
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 0a0e79ba11f..06a75a494d7 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -28,7 +28,7 @@ boltons==19.3.0
 boto3==1.9.114
 boto==2.49.0
 botocore==1.12.253
-bx-python==0.8.7
+bx-python==0.8.8
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
 cachetools==3.1.1