From caa82c33d5a7212956889a3741fe1ac82863fea7 Mon Sep 17 00:00:00 2001
From: Thomas Cokelaer <cokelaer@gmail.com>
Date: Mon, 22 May 2023 16:27:33 +0200
Subject: [PATCH] Fix installation adding bash shell

---
 .github/workflows/main.yml | 4 ++--
 README.rst                 | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6768801..6fd8935 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -36,8 +36,8 @@ jobs:
           extra-specs: |
             python=${{ matrix.python }}
 
-
-    - name: conda
+    - name: install package itself
+      shell: bash -l {0}
       run: |
         pip install .
 
diff --git a/README.rst b/README.rst
index a6cc1af..c304c62 100644
--- a/README.rst
+++ b/README.rst
@@ -39,7 +39,7 @@ Just install this package::
 
     pip install sequana_pacbio_qc
 
-You will need **kraken2** (optional) for the taxonomic analysis.
+You will need **samtools** and  **kraken2** (optional) for the taxonomic analysis.
 
 
 Usage
@@ -77,6 +77,7 @@ Requirements
 This pipelines requires the following executable(s):
 
 - sequana
+- samtools
 - kraken2
 - multiqc