From 4e7cfffb6f6380bcd091802da4cc27eb050f7a6e Mon Sep 17 00:00:00 2001
From: Michael Hall <michael@mbh.sh>
Date: Wed, 18 Oct 2023 12:23:51 +1000
Subject: [PATCH] ci: remove tmp steps

---
 .github/workflows/main.yml | 11 -----------
 bin/snippy                 |  4 ++--
 2 files changed, 2 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 8917b67..cae261d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -10,11 +10,6 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v4
 
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v3
-      with:
-        detached: true
-
     - name: Install Dependencies
       run: |
         sudo apt-get update
@@ -31,12 +26,6 @@ jobs:
         ! (ldd $PWD/binaries/linux/samtools  | grep 'not found')
         ! (ldd $PWD/binaries/linux/bcftools  | grep 'not found')
 
-    # the check snippy step keeps erroring with /usr/bin/env: ‘perl’: Not a directory so check the perl installation
-    - name: Check perl installation
-      run: |
-        perl --version
-        which perl
-
     - name: Check snippy versions and configurations
       run: |
         snippy --version
diff --git a/bin/snippy b/bin/snippy
index cfd8512..1e63b41 100755
--- a/bin/snippy
+++ b/bin/snippy
@@ -94,12 +94,12 @@ sub parse_version {
   #msg("parse=[$blob]");
   $blob =~ $re;
   my $ver = defined $1 ? $1 : 0;
-  err("Need $cmd >= $min but you have $ver - please upgrade it. VER=$blob 1=$1")
+  err("Need $cmd >= $min but you have $ver - please upgrade it.")
     if version->parse("v$ver") < version->parse("v$min");
   msg("Checking version: $cmd is >= $min - ok, have $ver");
   return $ver;
 }
-parse_version( 'samtools --version-only',   '1.7', qr/(\d+\.\d+)/ms );
+parse_version( 'samtools --version',   '1.7', qr/samtools\s(\d+\.\d+)/ms );
 parse_version( 'bcftools --version',   '1.7', qr/bcftools\s(\d+\.\d+)/ms );
 parse_version( 'freebayes --version',  '1.1', qr/\sv(\d+\.\d+.\d+)/ms    );
 parse_version( 'snpEff -version',      '4.3', qr/(\d+\.\d+)/ms           );