fix: containers and launch script (#31)

* update base image r version * install from github no deps update * fix launch scripts - correct hostname when in interactive session - mounting PWD
NBISweden · Jan 10, 2024 · bd7e524 · bd7e524
1 parent cd2c97e
commit bd7e524
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Showing 7 changed files with 9 additions and 9 deletions.
diff --git a/containers/dockerfiles/bioconductor_spatial.Dockerfile b/containers/dockerfiles/bioconductor_spatial.Dockerfile
@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:4.3.2
+FROM rocker/tidyverse:4.3.0
 
 ARG NCPUS=${NCPUS:--1}
 

diff --git a/containers/dockerfiles/seurat_spatial.Dockerfile b/containers/dockerfiles/seurat_spatial.Dockerfile
@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:4.3.2
+FROM rocker/tidyverse:4.3.0
 
 ARG NCPUS=${NCPUS:--1}
 

diff --git a/containers/scripts/install_bioconductor.sh b/containers/scripts/install_bioconductor.sh
@@ -68,7 +68,7 @@ installBioc.r --error --skipinstalled -n "$NCPUS" \
     tradeSeq
 
 ## Install R packages from GitHub
-installGithub.r \
+installGithub.r --update FALSE \
     https://github.com/powellgenomicslab/scPred/tree/af5492e778b076e529c20462c92aacd06c75bdc0 
 
 ## Clean up

diff --git a/containers/scripts/install_seurat.sh b/containers/scripts/install_seurat.sh
@@ -61,7 +61,7 @@ installBioc.r --error --skipinstalled -n "$NCPUS" \
     tradeSeq
 
 ## Install R packages from GitHub
-installGithub.r \
+installGithub.r --update FALSE \
     https://github.com/chris-mcginnis-ucsf/DoubletFinder/tree/1b1d4e2d7f893a3552d9f8f791ab868ee4c782e6 \
     https://github.com/immunogenomics/harmony/tree/f054b030b5d503e7c385dac6290604013ab9f81b \
     https://github.com/powellgenomicslab/scPred/tree/af5492e778b076e529c20462c92aacd06c75bdc0

diff --git a/containers/scripts/install_seurat_spatial.sh b/containers/scripts/install_seurat_spatial.sh
@@ -46,10 +46,10 @@ installBioc.r --error --skipinstalled -n "$NCPUS" \
     Biobase
 
 ## Install packages from GitHub
-installGithub.r \
+installGithub.r --update FALSE \
     https://github.com/renozao/xbioc/tree/1354168bd7e64be4ee1f9f74e971a61556d75003 \
     https://github.com/meichendong/SCDC/tree/890c604eebd7fffa4a08d7344fbd516df6efcf8d \
-    https://github.com/satijalab/seurat-data/tree/dd7d0df1fe7cd563281eac91edd0f1fac1ff3fe5
+    https://github.com/satijalab/seurat-data/tree/d6a8ce61ccb21a3b204f194d07009772c822791d
 
 ## Clean up
 rm -rf /var/lib/apt/lists/*

diff --git a/containers/uppmax/launch_jupyter.sh b/containers/uppmax/launch_jupyter.sh
@@ -18,7 +18,7 @@ cat 1>&2 <<END
 
 1. SSH tunnel from your workstation using the following command:
 
-   ssh -N -L 8888:${HOSTNAME}:${PORT} ${APPTAINERENV_USER}@${HOSTNAME}
+   ssh -N -L 8888:$(hostname):${PORT} ${APPTAINERENV_USER}@${HOSTNAME}
 
    point your web browser to http://localhost:8888/lab
 
@@ -35,7 +35,7 @@ When done using Jupyter, terminate the job by:
 
 END
 
-apptainer exec --bind /home/susanner/projects/workshop-scrnaseq:/run/user ${SIF} \
+apptainer exec --bind ${PWD}:/run/user ${SIF} \
     /usr/local/bin/start.sh \
     jupyter lab \
         --no-browser \

diff --git a/containers/uppmax/launch_rstudio.sh b/containers/uppmax/launch_rstudio.sh
@@ -55,7 +55,7 @@ cat 1>&2 <<END
 
 1. SSH tunnel from your workstation using the following command:
 
-   ssh -N -L 8787:${HOSTNAME}:${PORT} ${APPTAINERENV_USER}@${HOSTNAME}
+   ssh -N -L 8787:$(hostname):${PORT} ${APPTAINERENV_USER}@${HOSTNAME}
 
    and point your web browser to http://localhost:8787