From a24d9bf85ca7f5cc52ebc2c64bcd3e42927c023d Mon Sep 17 00:00:00 2001
From: martinghunt <martinghunt@users.noreply.github.com>
Date: Wed, 27 Sep 2023 16:10:04 +0100
Subject: [PATCH] git clone mccortex v0.0.5 from Mykrobe-tools/mccortex (#179)

---
 .github/workflows/build.yaml | 4 ++--
 Dockerfile                   | 4 ++--
 ci/install_mykrobe_linux.sh  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 5f28433..f064c62 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -105,7 +105,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex mccortex
+        git clone -b v0.0.5 --recursive https://github.com/Mykrobe-tools/mccortex mccortex
         cd mccortex
         make MAXK=31
         cd ..
@@ -185,7 +185,7 @@ jobs:
 
         echo "clone mccortex"
         rm -rf mccortex
-        git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex
+        git clone -b v0.0.5 --recursive https://github.com/Mykrobe-tools/mccortex mccortex
         cd mccortex/libs/htslib
         git checkout bcf9bff178f81c9c1cf3a052aeb6cbe32fe5fdcc
         cd ../bcftools
diff --git a/Dockerfile b/Dockerfile
index bf69d36..2bbfaf3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -33,7 +33,7 @@ COPY . "/${PROJECT}"
 # install mccortex
 WORKDIR "/tmp"
 
-RUN git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex \
+RUN git clone -b v0.0.5 --recursive https://github.com/Mykrobe-tools/mccortex mccortex \
     && cd mccortex \
     && make MAXK=31 \
     && cp bin/mccortex31 /${PROJECT}/src/mykrobe/cortex/ \
@@ -45,4 +45,4 @@ RUN python -m pip install requests && python -m pip install . -vv
 
 # download panels
 RUN mykrobe panels update_metadata \
-    && mykrobe panels update_species all
\ No newline at end of file
+    && mykrobe panels update_species all
diff --git a/ci/install_mykrobe_linux.sh b/ci/install_mykrobe_linux.sh
index b7b432e..040a85e 100755
--- a/ci/install_mykrobe_linux.sh
+++ b/ci/install_mykrobe_linux.sh
@@ -23,7 +23,7 @@ python -m pip install -U pip
 
 cd $MYKROBE_ROOT_DIR
 rm -rf mccortex
-git clone --recursive -b geno_kmer_count https://github.com/Mykrobe-tools/mccortex mccortex
+git clone -b v0.0.5 --recursive https://github.com/Mykrobe-tools/mccortex mccortex
 cd mccortex
 make
 cd ..