Merge pull request #11 from tinavisnovska/master

dev update: upgrading singularity to v3.

Author: sigven

README.md

@@ -61,7 +61,7 @@ An installation of Python (version >=_3.6_) is required to run *gvanno*. Check t
 
 ##### 1.1: Installation of Singularity (optional)
 
-0. **Note: this has only been tested with Singularity version 2.4.2, your mileage may vary with other versions**.
+0. **Note: this works for Singularity version 3.0 and higher**.
 1. [Install Singularity](https://sylabs.io/docs/)
 2. Test that singularity works by running `singularity --version`
 3. If you are in the gvanno directory, build the singularity image like so:

gvanno.py

@@ -282,15 +282,15 @@ def run_gvanno(arg_dict, host_directories):
    if arg_dict['container'] == 'docker':
       container_command_run1 = container_command_run1 + " -w=/workdir/output " + str(DOCKER_IMAGE_VERSION) + " sh -c \""
    elif arg_dict['container'] == 'singularity':
-      container_command_run1 = container_command_run1 + " -W /workdir/output " + 'src/gvanno.simg' + " sh -c \""
+      container_command_run1 = container_command_run1 + " -W /workdir/output " + 'src/gvanno.sif' + " sh -c \""
 
    if arg_dict['container'] == 'docker':
       container_command_run2 = "docker run --rm -t -u " + str(uid) + " -v=" +  str(databundle_volume_mapping) + " -v=" + str(output_volume_mapping)
       container_command_run2 = container_command_run2 + " -w=/workdir/output " + str(DOCKER_IMAGE_VERSION) + " sh -c \""
       docker_command_run_end = '\"'
    elif arg_dict['container'] == 'singularity':
       container_command_run2 = "singularity exec " + " -B " +  str(databundle_volume_mapping) + " -B " + str(output_volume_mapping)
-      container_command_run2 = container_command_run2 + " -W /workdir/output " + 'src/gvanno.simg' + " sh -c \""
+      container_command_run2 = container_command_run2 + " -W /workdir/output " + 'src/gvanno.sif' + " sh -c \""
       docker_command_run_end = '\"'
 
    ## GVANNO|start - Log key information about sample, options and assembly

src/buildSingularity.sh

@@ -24,19 +24,8 @@ docker build -t gvanno .
 docker tag gvanno localhost:5000/gvanno
 docker push localhost:5000/gvanno
 
-# create a temporary singularity def file
-declare -r TMPFILE="$(mktemp --suffix 'singularity.def')"
-cat > "$TMPFILE" << EOI
-Bootstrap: docker
-Registry: http://localhost:5000
-Namespace:
-From: gvanno:latest
-EOI
-# build singularity image
-sudo SINGULARITY_NOHTTPS=1 singularity build gvanno.simg "$TMPFILE"
-
-# remove temp file
-rm -f "$TMPFILE"
+# build singularity image from the docker cached local gvanno image
+sudo SINGULARITY_NOHTTPS=1 singularity build gvanno.sif docker-daemon://gvanno:latest
 
 # stop registry server
 docker container stop registry