Update conda and docker install, better load .fq files

.gitlab-ci.yml

@@ -5,19 +5,20 @@ stages:
   
 
 services:
-  - docker:dind
+  - registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:dind
 
 variables:
   DOCKER_HOST: tcp://localhost:2375
 
 
 build_dev:
-  image: docker:latest
+  image: registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:latest
   stage: build_dev
   variables:
     CI_DEBUG_TRACE: "false"
   script:
     - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
+    # - docker pull aghozlane/shaman:latest || true
     - docker build 
       --tag "$CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA"
       .
@@ -27,12 +28,13 @@ build_dev:
     - master
 
 build_master:
-  image: docker:latest
+  image: registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:latest
   stage: build_master
   variables:
     CI_DEBUG_TRACE: "false"
   script:
     - docker login -u "$DOCKER_USER" -p "$DOCKER_PASS"
+    # - docker pull aghozlane/shaman:latest || true
     - docker build -t aghozlane/shaman .
     - docker push aghozlane/shaman
   only:
@@ -51,6 +53,7 @@ build_conda:
     - conda config --add channels r
     - conda config --add channels aghozlane
     - conda config --set anaconda_upload yes
+    - conda update conda
     - conda install -y conda-verify
     - conda install -y anaconda-client
     - conda install -y conda-build

ui.R

@@ -415,7 +415,7 @@ function(request) {
                                  # br(),
                                  column(width=12,
                                         
-                                        fileInput("dir",label = 'Select your fastq files',accept = c(".fastq,.fastq.gz,.fgz,.gz"),multiple = TRUE),
+                                        fileInput("dir",label = 'Select your fastq files',accept = c(".fastq,.fastq.gz,.fq,.fq.gz"),multiple = TRUE),
                                         # shinyDirButton("dir", "Select a directory", "Upload",buttonType = "primary")
                                         
                                         # tags$input(id = "dir2", webkitdirectory = TRUE, type = "file", onchange="pressed()"),