search

genomehubs / demo

Example configurations to set up custom Ensembl sites using GenomeHubs
genomehubs.org
MIT License
2 stars 2 forks source link

Can't import local files #8

Open DuraSnow opened 5 years ago

DuraSnow commented 5 years ago

problem like this: cp: cannot stat '/genomehubs/Phytozome/PhytozomeV12_unrestricted/Ptrichocarpa/v3.0/annotation/Ptrichocarpa_210_v3.0.gene.gff3.gz': No such file or directory ERROR: could not cp /genomehubs/Phytozome/PhytozomeV12_unrestricted/Ptrichocarpa/v3.0/annotation/Ptrichocarpa_210_v3.0.gene.gff3.gz to Ptrichocarpa_210_v3.0.gene.gff3.gz preparing gff cp: cannot stat '/genomehubs/Phytozome/PhytozomeV12_unrestricted/Ptrichocarpa/v3.0/annotation/Ptrichocarpa_210_v3.0.gene.gff3.gz': No such file or directory ERROR: could not cp /genomehubs/Phytozome/PhytozomeV12_unrestricted/Ptrichocarpa/v3.0/annotation/Ptrichocarpa_210_v3.0.gene.gff3.gz to Ptrichocarpa_210_v3.0.gene.gff3.gz importing gene models cp: cannot stat '/genomehubs/Phytozome/PhytozomeV12_unrestricted/Ptrichocarpa/v3.0/annotation/Ptrichocarpa_210_v3.0.gene.gff3.gz': No such file or directory ERROR: could not cp /genomehubs/Phytozome/PhytozomeV12_unrestricted/Ptrichocarpa/v3.0/annotation/Ptrichocarpa_210_v3.0.gene.gff3.gz to Ptrichocarpa_210_v3.0.gene.gff3.gz verifying import

rjchallis commented 5 years ago

The path to Ptrichocarpa_210_v3.0.gene.gff3.gz can either be a remote URL or a path that is available in the container filesystem. Just looking back at the docs I realise that the example files use a remote URL so I'll need to fix this and make sure there is an example for using local files.

In the docker run command, you need to mount a local directory to /import/data so you can keep the log files, etc. that are created during the import. These files will all be written to a subdirectory matching the core database name. If you are happy to have that subdirectory created alongside your existing data, you can mount your existing data directory using the -v option:

docker run \
    ... \
    -v /genomehubs/Phytozome/PhytozomeV12_unrestricted/Ptrichocarpa/v3.0:/import/data \
    ...

Then change the file path in your config file to:

[FILES]
    GFF = [ gff3 /import/data/annotation/Ptrichocarpa_210_v3.0.gene.gff3.gz ]

If you would prefer to keep these files elsewhere on your filesystem then mount a different directory to /import/data where the new files will be written and mount your data directory elsewhere on the container (e.g. /tmp/data) and change the file path in the config accordingly.

DuraSnow commented 5 years ago

ths，I’ll try

Richard Challis notifications@github.com于2019年1月7日 周一下午5:25写道：

The path to Ptrichocarpa_210_v3.0.gene.gff3.gz can either be a remote URL or a path that is available in the container filesystem. Just looking back at the docs I realise that the example files use a remote URL so I'll need to fix this and make sure there is an example for using local files.

In the docker run command, you need to mount a local directory to /import/data so you can keep the log files, etc. that are created during the import. These files will all be written to a subdirectory matching the core database name. If you are happy to have that subdirectory created alongside your existing data, you can mount your existing data directory using the -v option:

docker run \ ... \ -v /genomehubs/Phytozome/PhytozomeV12_unrestricted/Ptrichocarpa/v3.0:/import/data \ ...

Then change the file path in your config file to:

[FILES] GFF = [ gff3 /import/data/annotation/Ptrichocarpa_210_v3.0.gene.gff3.gz ]

If you would prefer to keep these files elsewhere on your filesystem then mount a different directory to /import/data where the new files will be written and mount your data directory elsewhere on the container (e.g. /tmp/data) and change the file path in the config accordingly.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/genomehubs/demo/issues/8#issuecomment-451872307, or mute the thread https://github.com/notifications/unsubscribe-auth/AOQbHx4nxXsoTjMpSDt7LkGb1_qZWJuxks5vAxJ3gaJpZM4ZlBvm .