diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 67ae263fdfddedb371bc98af7e8212a0312df891..c1aadaca0ec4e743f40da3a53dd7913af64cb5e6 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,30 +1,11 @@ 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: diff --git a/Dockerfile_redhat_autotools b/Dockerfile_redhat_autotools new file mode 100644 index 0000000000000000000000000000000000000000..f15021c624c1568c0746b501b53fe2ba291c9acc --- /dev/null +++ b/Dockerfile_redhat_autotools @@ -0,0 +1,16 @@ +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 diff --git a/README.md b/README.md index 0d6c2be2e01494ba792fb1bd4672e4f486f00a87..599983255e35ca68df31f27deed11e913fa02246 100644 --- a/README.md +++ b/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 + +Ãlvarez-Pérez S, Quevedo-Caraballo S, GarcÃa 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) diff --git a/run_tests_ci.sh b/run_tests_ci.sh new file mode 100755 index 0000000000000000000000000000000000000000..7910c60b5104f4e14ce240a249418999e4f97a44 --- /dev/null +++ b/run_tests_ci.sh @@ -0,0 +1,20 @@ +#!/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