From a474c0dff8ce75ad2e93f2c10047c7f9518b292f Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Wed, 22 Nov 2023 16:50:52 +0100
Subject: [PATCH 1/4] Update Hapo-G from 1.3.6 to 1.3.7

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

diff --git a/tools/hapog/hapog.xml b/tools/hapog/hapog.xml
index ed8f885459d..8ec8c35526e 100644
--- a/tools/hapog/hapog.xml
+++ b/tools/hapog/hapog.xml
@@ -1,21 +1,21 @@
 <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>genome polishing</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.3.6</token>
+        <token name="@TOOL_VERSION@">1.3.7</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
     </requirements>
+    <xrefs>
+        <xref type="bio.tools">hapog</xref>
+    </xref>
     <command detect_errors="exit_code"><![CDATA[
 hapog
 --genome '${genome}'
 --output output/
 
-## setting default threads to 2 until
-## https://github.com/institut-de-genomique/HAPO-G/issues/34
-## gets addressed, at least
---threads \${GALAXY_SLOTS:-2}
+--threads \${GALAXY_SLOTS:-1}
 
 #if str( $reads.type ) == "short":
     #for $i in $reads.pe1

From 3b1d5111e3ed0859124918d30f5a646f47303f34 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 22 Nov 2023 19:15:02 +0100
Subject: [PATCH 2/4] Update hapog.xml

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

diff --git a/tools/hapog/hapog.xml b/tools/hapog/hapog.xml
index 8ec8c35526e..d5b4ac839ed 100644
--- a/tools/hapog/hapog.xml
+++ b/tools/hapog/hapog.xml
@@ -9,7 +9,7 @@
     </requirements>
     <xrefs>
         <xref type="bio.tools">hapog</xref>
-    </xref>
+    </xrefs>
     <command detect_errors="exit_code"><![CDATA[
 hapog
 --genome '${genome}'

From 7353a9eb2ae648486dacb3da97bfdeb231c665bd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 22 Nov 2023 20:36:03 +0100
Subject: [PATCH 3/4] Update hapog.xml

---
 tools/hapog/hapog.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/hapog/hapog.xml b/tools/hapog/hapog.xml
index d5b4ac839ed..f52e4825f44 100644
--- a/tools/hapog/hapog.xml
+++ b/tools/hapog/hapog.xml
@@ -4,12 +4,12 @@
         <token name="@TOOL_VERSION@">1.3.7</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
-    </requirements>
     <xrefs>
         <xref type="bio.tools">hapog</xref>
     </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
+    </requirements>
     <command detect_errors="exit_code"><![CDATA[
 hapog
 --genome '${genome}'

From c36884ff8d400a1dedb47ae8c79b20aa1904255e Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Sun, 28 Jan 2024 18:05:29 +0100
Subject: [PATCH 4/4] Scale memory assignment to samtools

---
 tools/hapog/hapog.xml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tools/hapog/hapog.xml b/tools/hapog/hapog.xml
index f52e4825f44..75487bc7712 100644
--- a/tools/hapog/hapog.xml
+++ b/tools/hapog/hapog.xml
@@ -11,11 +11,16 @@
         <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+##Compute samtools memory settings like in samtools_sort
+##use only 75% of available: https://github.com/samtools/samtools/issues/831
+addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
+((addmemory=addmemory*75/100)) &&
 hapog
 --genome '${genome}'
 --output output/
 
 --threads \${GALAXY_SLOTS:-1}
+--samtools-mem \$addmemory"M"
 
 #if str( $reads.type ) == "short":
     #for $i in $reads.pe1