more unhelpful changes

dev.sh

@@ -47,29 +47,29 @@ export SINGULARITY_CACHEDIR=/tmp
 #   chmod -R 770 $PWD/mongodb/data/db
 # fi
 
-# if [ ! -f $PWD/mongodb/mongodb.sif ]; then # Will eventually be redundant and can remove
-#     echo "building mongodb"
-#     # build image
-#     singularity build           \
-#       --arch "amd64"            \
-#       --fakeroot                \
-#       --disable-cache           \
-#       $PWD/mongodb/mongodb.sif  \
-#       $PWD/mongodb/Singularity
+if [ ! -f $PWD/mongodb/mongodb.sif ]; then # Will eventually be redundant and can remove
+    echo "building mongodb"
+    # build image
+    singularity build           \
+      --arch "amd64"            \
+      --fakeroot                \
+      --disable-cache           \
+      $PWD/mongodb/mongodb.sif  \
+      $PWD/mongodb/Singularity
 
-#     # start the container instance
-#     singularity instance start  \
-#       --fakeroot                \
-#       --bind $PWD/mongodb/data/db:/data/db \
-#       $PWD/mongodb/mongodb.sif  \
-#       brainlife_ezbids-mongodb
-
-
-#       # --net \
-#       # --network-args "portmap=27417:27017/tcp"  \
-#       # --bind $PWD/data/db:/data/db \  # Might not need this if mongodb/Singularity contains a %files section
-#     # singularity run instance://brainlife_ezbids-mongodb # This seems to run mongodb in the foreground, meaning can't move on to building other containers.
-# fi
+    # start the container instance
+    singularity instance start  \
+      --fakeroot                \
+      --bind $PWD/mongodb/data/db:/data/db \
+      $PWD/mongodb/mongodb.sif  \
+      brainlife_ezbids-mongodb
+
+
+      # --net \
+      # --network-args "portmap=27417:27017/tcp"  \
+      # --bind $PWD/data/db:/data/db \  # Might not need this if mongodb/Singularity contains a %files section
+    # singularity run instance://brainlife_ezbids-mongodb # This seems to run mongodb in the foreground, meaning can't move on to building other containers.
+fi
 
 # if [ ! -f $PWD/api/api.sif ]; then
 #     echo "building api"
@@ -93,10 +93,10 @@ export SINGULARITY_CACHEDIR=/tmp
 
 
 
-# Approach #2: singularity-compose 
+# # Approach #2: singularity-compose 
 
-if [ ! -d $PWD/mongodb/data/db ]; then
-    mkdir -p $PWD/mongodb/data/db
-    chmod -R 770 $PWD/mongodb/data/db
-fi
-singularity-compose --debug up --no-resolv
+# # if [ ! -d $PWD/mongodb/data/db ]; then
+# #     mkdir -p $PWD/mongodb/data/db
+# #     chmod -R 770 $PWD/mongodb/data/db
+# # fi
+# singularity-compose --debug up --no-resolv

mongodb/Singularity

@@ -1,13 +1,16 @@
 Bootstrap: docker
 From: mongo:4.4.15
 
-# %environment
-# export HOME=$PWD/data/db
+%environment
+export HOME=/data/db
+export PWD=/
 
 %runscript
     # mongod --dbpath $PWD/data/db
+    cd $HOME
     exec /usr/bin/mongod "$@"
 
 %startscript
     # mongod --dbpath $PWD/data/db
+    cd $HOME
     exec /usr/bin/mongod "$@"

singularity-compose.yml

@@ -12,7 +12,6 @@ instances:
     #     post:
     #         command:
     #             - "mongod --dbpath /tmp"
-    #         # command: ["mongod --dbpath /tmp"]
 
     # mongodb:  # NEW BUT STILL BAD
     #     container_name: brainlife_ezbids-mongodb
@@ -54,9 +53,6 @@ instances:
         # start:
         #     options:
         #         - fakeroot
-        post:
-            command: mongod --dbpath /data/db
-            # command: echo 'db.runCommand("ping").ok' | mongo localhost:27017/test --quiet
         # run:
         #     background: true # Does this actually run things in the background? Doesn't seem to