From 4557d75f5a9beee25dcbd250f6df0b084f3dcf1c Mon Sep 17 00:00:00 2001
From: Marina Gourtovaia <mg8@sanger.ac.uk>
Date: Fri, 13 Oct 2023 09:25:08 +0100
Subject: [PATCH] Removed redundant CI script.

---
 .github/workflows/run-tests.yml | 1 -
 MANIFEST                        | 1 -
 scripts/before_install.sh       | 8 --------
 t/autoqc_util.pm                | 4 ++--
 4 files changed, 2 insertions(+), 12 deletions(-)
 delete mode 100755 scripts/before_install.sh

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 2962c4b8..c378dcb0 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -93,7 +93,6 @@ jobs:
       - name: "NPM"
         run: |
           mkdir -p "$NPM_CONFIG_PREFIX"
-          ${GITHUB_WORKSPACE}/scripts/before_install.sh
 
       - name: "Install Perl dependencies"
         run: |
diff --git a/MANIFEST b/MANIFEST
index 3c74d716..6ac8f04b 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -166,7 +166,6 @@ lib/npg_qc/utils/bam_genotype.pm
 lib/npg_qc/utils/genotype_calling.pm
 MANIFEST
 README
-scripts/before_install.sh
 scripts/npgqc_dbix_schema_loader.pl
 t/00-critic.t
 t/00-distribution.t
diff --git a/scripts/before_install.sh b/scripts/before_install.sh
deleted file mode 100755
index c0d3713e..00000000
--- a/scripts/before_install.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-set -e -x -u
-
-# Dummy executable files generated for tests use #!/usr/local/bin/bash
-sudo mkdir -p /usr/local/bin
-sudo ln -s /bin/bash /usr/local/bin/bash
-/usr/local/bin/bash --version
diff --git a/t/autoqc_util.pm b/t/autoqc_util.pm
index ad20a362..4777c6d5 100644
--- a/t/autoqc_util.pm
+++ b/t/autoqc_util.pm
@@ -77,7 +77,7 @@ sub write_seqtk_script {
   my $fh;
   open($fh, '>', $script_path) or croak "Cannot open $script_path for writing";
 
-  print $fh '#!/usr/local/bin/bash';
+  print $fh '#!/usr/bin/env bash';
   print $fh "\n";
   print $fh '# Script to fake seqtk in testing. Automatically generated by npg at ' . time;
   print $fh "\n";
@@ -108,7 +108,7 @@ sub write_bwa_script {
   my $fh;
   open($fh, '>', $script_path) or croak "Cannot open $script_path for writing";
 
-  print $fh '#!/usr/local/bin/bash';
+  print $fh '#!/usr/bin/env bash';
   print $fh "\n";
   print $fh '# Script to fake BWA tool in testing. Automatically generated by npg at ' . time;
   print $fh "\n";