From e6a94e92c1d8d24f9fe021d2dd8fda9a43beb28b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 12 Apr 2024 20:28:17 +0200
Subject: [PATCH 1/7] Fix containerized merqury

Might be faster than https://github.com/bioconda/bioconda-recipes/pull/47201
---
 tools/merqury/macros.xml                     | 4 +++-
 tools/merqury/test-data/output_06_qv.tabular | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/tools/merqury/macros.xml b/tools/merqury/macros.xml
index f5a92a84403..36f00331b53 100644
--- a/tools/merqury/macros.xml
+++ b/tools/merqury/macros.xml
@@ -11,7 +11,9 @@
             <requirement type="package" version="@TOOL_VERSION@">merqury</requirement>
             <requirement type="package" version="1.34">tar</requirement>
             <requirement type="package" version="4.6.0">findutils</requirement>
-            <requirement type="package" version="8.32">coreutils</requirement>
+            <requirement type="package" version="9.5">coreutils</requirement>
+            <requirement type="package" version="4.8">sed</requirement>
+            <requirement type="package" version="5.3.0">gawk</requirement>
         </requirements>
     </xml>
     <xml name="citations">
diff --git a/tools/merqury/test-data/output_06_qv.tabular b/tools/merqury/test-data/output_06_qv.tabular
index d92d673f4d8..ec8513158dc 100644
--- a/tools/merqury/test-data/output_06_qv.tabular
+++ b/tools/merqury/test-data/output_06_qv.tabular
@@ -1,2 +1,2 @@
 assembly	unique k-mers	common k-mers	QV	error rate
-assembly	0	1037953		
+assembly	0	1037953	+inf	0

From 17b6dd4232cc7f238131a4d7b6420bf625f8844c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 12 Apr 2024 21:59:08 +0200
Subject: [PATCH 2/7] remove upstream deps

---
 tools/merqury/macros.xml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/merqury/macros.xml b/tools/merqury/macros.xml
index 36f00331b53..4be15893810 100644
--- a/tools/merqury/macros.xml
+++ b/tools/merqury/macros.xml
@@ -12,8 +12,6 @@
             <requirement type="package" version="1.34">tar</requirement>
             <requirement type="package" version="4.6.0">findutils</requirement>
             <requirement type="package" version="9.5">coreutils</requirement>
-            <requirement type="package" version="4.8">sed</requirement>
-            <requirement type="package" version="5.3.0">gawk</requirement>
         </requirements>
     </xml>
     <xml name="citations">

From 8a30c13a24ff997df168182ef0c9bedb175c2f07 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 13 Apr 2024 17:41:49 +0200
Subject: [PATCH 3/7] fix container init

---
 tools/merqury/merqury_plot_CN.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/merqury/merqury_plot_CN.xml b/tools/merqury/merqury_plot_CN.xml
index 85349b36406..5e491bdcdcf 100644
--- a/tools/merqury/merqury_plot_CN.xml
+++ b/tools/merqury/merqury_plot_CN.xml
@@ -6,9 +6,9 @@
     <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <version_command>merqury --version</version_command>
-
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p output_files/ &&
+        export MERQURY="\$(dirname \$(which merqury.sh))/../share/merqury" &&
         \$MERQURY/plot/plot_spectra_cn.R 
         -f '$input1' 
         -o output_files/merqury_plot

From a9bbe1082b593839dd0482957f9365a5b309d620 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 13 Apr 2024 17:42:29 +0200
Subject: [PATCH 4/7] update test data, its a bit concerning why this has
 changed

---
 tools/merqury/test-data/output_02_qv.tabular | 2 +-
 tools/merqury/test-data/output_03_qv.tabular | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/merqury/test-data/output_02_qv.tabular b/tools/merqury/test-data/output_02_qv.tabular
index 23a7e64b348..7c9ab742f92 100644
--- a/tools/merqury/test-data/output_02_qv.tabular
+++ b/tools/merqury/test-data/output_02_qv.tabular
@@ -1 +1 @@
-assembly	0	1037953		
+assembly	0	1037953	+inf	0
diff --git a/tools/merqury/test-data/output_03_qv.tabular b/tools/merqury/test-data/output_03_qv.tabular
index f86d4e65303..b0f077a240d 100644
--- a/tools/merqury/test-data/output_03_qv.tabular
+++ b/tools/merqury/test-data/output_03_qv.tabular
@@ -1,3 +1,3 @@
-assembly_01	0	1037953		
-assembly_02	0	1037953		
-Both	0	2075906		
+assembly_01	0	1037953	+inf	0
+assembly_02	0	1037953	+inf	0
+Both	0	2075906	+inf	0

From d4116f35f596a8045d68fd4d85bdedafa7ad6f2e Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 13 Apr 2024 17:49:31 +0200
Subject: [PATCH 5/7] fix last test

---
 tools/merqury/merqury.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/merqury/merqury.xml b/tools/merqury/merqury.xml
index 2583733e0a9..9fbc06c7997 100644
--- a/tools/merqury/merqury.xml
+++ b/tools/merqury/merqury.xml
@@ -236,7 +236,7 @@
             <output_collection name="png_files" type="list" count="6">
                 <element name="output_02.assembly.spectra-cn.fl">
                     <assert_contents>
-                        <has_size value="71874" delta="100"/>
+                        <has_size value="74570" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.assembly.spectra-cn.ln">

From 0db03a9f1c31d06c87240005e42e8a7106a33a5f Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 13 Apr 2024 19:57:27 +0200
Subject: [PATCH 6/7] fix last tests

---
 tools/merqury/merqury.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/merqury/merqury.xml b/tools/merqury/merqury.xml
index 9fbc06c7997..7f6afb5df3d 100644
--- a/tools/merqury/merqury.xml
+++ b/tools/merqury/merqury.xml
@@ -241,27 +241,27 @@
                 </element>
                 <element name="output_02.assembly.spectra-cn.ln">
                     <assert_contents>
-                        <has_size value="71888" delta="100"/>
+                        <has_size value="74476" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.assembly.spectra-cn.st">
                     <assert_contents>
-                        <has_size value="71123" delta="100"/>
+                        <has_size value="74205" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.fl">
                     <assert_contents>
-                        <has_size value="47245" delta="100"/>
+                        <has_size value="48524" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.ln">
                     <assert_contents>
-                        <has_size value="46896" delta="100"/>
+                        <has_size value="48028" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.st">
                     <assert_contents>
-                        <has_size value="45945" delta="100"/>
+                        <has_size value="47447" delta="100"/>
                     </assert_contents>
                 </element>
             </output_collection>

From e5fa216f8d76bc2fe696927f139764b72d4c4869 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sat, 13 Apr 2024 20:21:54 +0200
Subject: [PATCH 7/7] Update macros.xml

---
 tools/merqury/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/merqury/macros.xml b/tools/merqury/macros.xml
index 4be15893810..add263d6a43 100644
--- a/tools/merqury/macros.xml
+++ b/tools/merqury/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">merqury</xref>