trouble with running on windows 10

[acpandey]

i am trying to run too-many-cells on windows 10. I am trying to do it with docker and used a lot of tips from previous issue #9, which was really helpful, but i seem to have hit a different error now. Any help would be greatly appreciated. thanks!

PS C:\Users\acpan\too-many-cells> docker run -i --rm -v C:\Users\acpan\too-many-cells\filtered_feature_bc_matrix\:/filtered_feature_bc_matrix/ gregoryschwartz/too-many-cells:0.2.2.0 make-tree --no-filter --normalization NoneNorm --draw-max-node-size 40 --draw-max-leaf-node-size 70 --matrix-path /filtered_feature_bc_matrix/matrix.mtx --output /filtered_feature_bc_matrix/out --labels-file /filtered_feature_bc_matrix/labels.csv
Loading matrix [..........................................................]   0%too-many-cells: CsvParseException "parse error (endOfInput)"
CallStack (from HasCallStack):
  error, called at src/TooManyCells/Matrix/Load.hs:220:27 in too-many-cells-0.2.2.0-AeD17o0PQYl1Xrk9gmUYF3:TooManyCells.Matrix.Load
PS C:\Users\acpan\too-many-cells> docker info
Client:
 Debug Mode: false
 Plugins:
  app: Docker Application (Docker Inc., v0.8.0)
  buildx: Build with BuildKit (Docker Inc., v0.3.1-tp-docker)
  mutagen: Synchronize files with Docker Desktop (Docker Inc., testing)

Server:
 Containers: 0
  Running: 0
  Paused: 0
  Stopped: 0
 Images: 1
 Server Version: 19.03.8
 Storage Driver: overlay2
  Backing Filesystem: <unknown>
  Supports d_type: true
  Native Overlay Diff: true
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
 Swarm: inactive
 Runtimes: runc
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 7ad184331fa3e55e52b890ea95e65ba581ae3429
 runc version: dc9208a3303feef5b3839f4323d9beb36df0a9dd
 init version: fec3683
 Security Options:
  seccomp
   Profile: default
 Kernel Version: 4.19.76-linuxkit
 Operating System: Docker Desktop
 OSType: linux
 Architecture: x86_64
 CPUs: 3
 Total Memory: 3.848GiB
 Name: docker-desktop
 ID: YF44:LHID:3WTQ:MWJL:RYGV:SOIO:E5PP:TAYH:VJWQ:7B2T:CNM7:2EJC
 Docker Root Dir: /var/lib/docker
 Debug Mode: true
  File Descriptors: 41
  Goroutines: 54
  System Time: 2020-05-28T20:45:40.026975263Z
  EventsListeners: 4
 Registry: https://index.docker.io/v1/
 Labels:
 Experimental: false
 Insecure Registries:
  127.0.0.0/8
 Live Restore Enabled: false
 Product License: Community Engine

[GregorySchwartz]

The csv parse error means that a csv was incorrectly parsed. Looking at your command, you specified the --matrix-path to matrix.mtx which is a file, not a directory. too-many-cells assumes a csv if the argument is a file and a matrix market file directory (which is what you have) if you specify a folder. So just delete the matrix.mtx and use the folder instead.

[acpandey]

The csv parse error means that a csv was incorrectly parsed. Looking at your command, you specified the --matrix-path to matrix.mtx which is a file, not a directory. too-many-cells assumes a csv if the argument is a file and a matrix market file directory (which is what you have) if you specify a folder. So just delete the matrix.mtx and use the folder instead.

thanks. this seems to have worked (ends suddenly while loading matrix). i think my current machine is running out of memory even though i tweaked the settings for docker. will try to see if i can do it on our hpc vs reducing the dataset first.

[GregorySchwartz]

Great!