Update for conda

.gitlab-ci.yml

@@ -34,3 +34,16 @@ build_master:
     - docker push aghozlane/shaman
   only:
     - master
+
+
+build_conda:
+    image: continuumio/miniconda3:latest
+    stage: build_conda
+    before_script:
+      - conda config --add channels bioconda
+      - conda config --add channels conda-forge
+      - conda config --add channels aghozlane
+      - conda config --set anaconda_upload yes
+    script:
+      - anaconda login --username "$DOCKER_USER" --password "$DOCKER_PASS"
+      - conda-build conda_inst
\ No newline at end of file

www/shaman_conda.R

-#!/usr/bin/Rscript --vanilla
+#!/usr/bin/env Rscript --vanilla
 prefix=Sys.getenv(x = "PREFIX")
 prefix=paste(prefix, "bin", sep=.Platform$file.sep)
 system(paste("python ", prefix, "shaman_bioblend/shaman_bioblend.py -w ", prefix,"shamanapp/www/masque/ -s -d", sep=.Platform$file.sep))
-system(paste("Rscript -e 'library(\"shiny\");runApp(appDir=", prefix,"KronaRShy\", port=5438)'", sep=.Platform$file.sep, wait=FALSE)
+system(paste(prefix, "Rscript -e 'library(\"shiny\");runApp(appDir=", prefix,"KronaRShy\", port=5438)'", sep=.Platform$file.sep, wait=FALSE)
 runApp(paste("appDir= ", prefix, "shamanapp", sep=.Platform$file.sep)