From 7ec84d18b9e5b4424b558bcb25b1459fcbe46294 Mon Sep 17 00:00:00 2001
From: Filipe Tostevin <filipe.tostevin@nanoporetech.com>
Date: Wed, 5 May 2021 10:47:02 +0100
Subject: [PATCH 1/2] install paftools from minimap to bin folder

---
 Makefile | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 53a2982..d9eef96 100644
--- a/Makefile
+++ b/Makefile
@@ -7,7 +7,7 @@ PYTHON      ?= python3
 CONDA       ?= ~/miniconda3/
 
 # Builds a cache of binaries which can just be copied for CI
-BINARIES=minimap2 miniasm racon samtools bcftools seqkit bedtools bgzip tabix
+BINARIES=minimap2 miniasm racon samtools bcftools paftools.js seqkit bedtools bgzip tabix
 
 BINCACHEDIR=bincache
 $(BINCACHEDIR):
@@ -79,6 +79,9 @@ $(BINCACHEDIR)/tabix: | $(BINCACHEDIR)/samtools
 $(BINCACHEDIR)/bgzip: | $(BINCACHEDIR)/samtools
 	cp ${BINBUILDDIR}/samtools-${SAMVER}/htslib-${SAMVER}/$(@F) $@
 
+$(BINCACHEDIR)/paftools.js: | $(BINCACHEDIR)/minimap2
+	cp ${BINBUILDDIR}/minimap2-${MAPVER}/misc/$(@F) $@
+
 
 BCFVER=1.7
 $(BINCACHEDIR)/bcftools: | $(BINCACHEDIR) $(BINBUILDDIR)

From 6fae61062f90e4d471aa767f6521fc0ff19b13fb Mon Sep 17 00:00:00 2001
From: Filipe Tostevin <filipe.tostevin@nanoporetech.com>
Date: Wed, 5 May 2021 11:10:58 +0100
Subject: [PATCH 2/2] install precompiled k8 (needed to run paftools)

---
 Makefile | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index d9eef96..6dea2c8 100644
--- a/Makefile
+++ b/Makefile
@@ -7,7 +7,7 @@ PYTHON      ?= python3
 CONDA       ?= ~/miniconda3/
 
 # Builds a cache of binaries which can just be copied for CI
-BINARIES=minimap2 miniasm racon samtools bcftools paftools.js seqkit bedtools bgzip tabix
+BINARIES=minimap2 miniasm racon samtools bcftools k8 paftools.js seqkit bedtools bgzip tabix
 
 BINCACHEDIR=bincache
 $(BINCACHEDIR):
@@ -79,6 +79,17 @@ $(BINCACHEDIR)/tabix: | $(BINCACHEDIR)/samtools
 $(BINCACHEDIR)/bgzip: | $(BINCACHEDIR)/samtools
 	cp ${BINBUILDDIR}/samtools-${SAMVER}/htslib-${SAMVER}/$(@F) $@
 
+K8VER=0.2.5
+$(BINCACHEDIR)/k8: | $(BINCACHEDIR) $(BINBUILDDIR)
+	@echo Making $(@F)
+	if [ ! -e ${BINBUILDDIR}/k8-${K8VER}.tar.bz2 ]; then \
+	  cd ${BINBUILDDIR}; \
+	  wget https://github.com/attractivechaos/k8/releases/download/${K8VER}/k8-${K8VER}.tar.bz2; \
+	  tar -xjf k8-${K8VER}.tar.bz2; \
+	fi
+	cp ${BINBUILDDIR}/k8-${K8VER}/k8-Linux $@
+
+
 $(BINCACHEDIR)/paftools.js: | $(BINCACHEDIR)/minimap2
 	cp ${BINBUILDDIR}/minimap2-${MAPVER}/misc/$(@F) $@