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Can't import local files #8
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The path to In the
Then change the file path in your config file to:
If you would prefer to keep these files elsewhere on your filesystem then mount a different directory to |
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.
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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
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