Merge branch 'master' of https://gitlab.pasteur.fr/vlegrand/ROCK

.gitlab-ci.yml

 makefile_generation_and_compilation_plus_run_nrt_tests_cluster:
-    image: registry-gitlab.pasteur.fr/dsi-tools/docker-images:centOS8_ROCK
+    image: docker:27
     script: 
-        - source /etc/profile.d/gensoft_modules.sh 
-        - module av
-        - module load gcc/7.2.0
-        - module load m4/1.4.17
-        - module load autoconf/2.69
-        - module load automake/1.15
-        - module list
-        - export PATH=$PATH:/usr/bin
-        - echo $PATH
-        - ls /usr/bin
-        - yum update -y && yum install -y perl perl-Thread-Queue.noarch && /usr/bin/perl --version
-        # - rm configure 
-        - aclocal
-        - autoconf -i
-        - automake
-        - ./configure
-        - make; cd src
-        - ./unit_test_fqreader
-        - ./unit_test_math_utils
-        - ./unit_test_fqwriter
-        - ./unit_test_cms
-        - ./unit_test_read_utils
-        - cd ..; make check
-        - make distcheck
+        - sleep 3 # Try to avoid "ERROR: open /certs/client/ca.pem: no such file or directory"
+        - docker build -t test_rh8.8_image -f Dockerfile_redhat_autotools .
+        - docker run -td -v $(pwd):/ROCK -w /ROCK --name test_all test_rh8.8_image 
+        - docker ps -a
+        - docker exec test_all sh -c "./run_tests_ci.sh"
         
 
 makefile_generation_and_compilation_plus_run_nrt_tests_ubuntu:

Dockerfile_redhat_autotools

+FROM redhat/ubi8:8.8
+RUN yum -y update && yum clean all
+RUN yum -y install wget sudo gcc gcc-c++ glibc-devel libstdc++.i686 glibc.i686 make perl which 
+RUN yum -y install procps-ng
+RUN echo [gensoft] > /etc/yum.repos.d/gensoft.repo
+RUN echo name=gensoft >> /etc/yum.repos.d/gensoft.repo
+RUN echo baseurl=http://mirrors.web.pasteur.fr/gensoft/c8/opt-rpm >> /etc/yum.repos.d/gensoft.repo
+RUN echo gpgcheck=0 >> /etc/yum.repos.d/gensoft.repo
+RUN yum update
+RUN yum install -y gensoft-modules-4.4.0 gensoft-gcc-9.2.0 gensoft-m4-1.4.18 gensoft-automake-1.16.3 gensoft-autoconf-2.69
+RUN source /etc/profile.d/gensoft_modules.sh && module load gcc/9.2.0 && gcc --version
+RUN source /etc/profile.d/gensoft_modules.sh && module load autoconf/2.69 && module list
+RUN source /etc/profile.d/gensoft_modules.sh && module load automake/1.16.3 && module list && perl --version
+RUN which perl
+RUN yum clean all
+RUN echo $PATH

README.md

@@ -326,3 +326,16 @@ Wedemeyer A, Kliemann L, Srivastav A, Schielke C, Reusch TB, Rosenstiel P (2017)
 ## Contributions
 
 Suggestions for improving _ROCK_ or for adding new functionalities, as well as merge requests, are welcome.
+
+
+## Citations
+
+Álvarez-Pérez S, Quevedo-Caraballo S, García ME, BlancoJL (2024)
+_Prevalence and genetic diversity of azole-resistant Malassezia pachydermatis isolates from canine otitis and dermatitis: A 2-year study_.
+**Medical Mycology**, 62:myae053.
+[doi:10.1093/mmy/myae053](https://doi.org/10.1093/mmy/myae053)
+
+Pottier M, Castagnet S, Gravey F, Leduc G, Sévin C, Petry S, Giard J-C, Le Hello S, Léon A (2022)
+_Antimicrobial Resistance and Genetic Diversity of Pseudomonas aeruginosa Strains Isolated from Equine and Other Veterinary Samples_.
+**Pathogens**, 12(1):64.
+[doi:10.3390/pathogens12010064](https://doi.org/10.3390/pathogens12010064)

run_tests_ci.sh

+#!/bin/sh
+source /etc/profile.d/gensoft_modules.sh || exit 1
+module av || exit 2
+module load gcc/9.2.0 || exit 3
+module load m4/1.4.18 || exit 4
+module load autoconf/2.69 || exit 5
+module load automake/1.16.3 || exit 6
+module list || exit 7
+aclocal || exit 8
+autoconf -i || exit 9
+automake || exit 10
+./configure || exit 11
+make; cd src || exit 12
+./unit_test_fqreader || exit 13
+./unit_test_math_utils || exit 14
+./unit_test_fqwriter || exit 15
+./unit_test_cms || exit 16
+./unit_test_read_utils || exit 17
+cd ..; make check || exit 18
+make distcheck || exit 19
\ No newline at end of file