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boutroslab / cld_docker

Docker for CRISPR Library Designer | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0915-2
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Could CLD work for the organisms which genomes are from plant Ensembl? #15

Open Xiaofei-git opened 1 year ago

Xiaofei-git commented 1 year ago

Dear @tonyreina

I supposed CLD should work for the genome from plant Ensembl by feeding --rsync-link, but it didn't. Please refer to the message below.

Thanks a lot!

$ docker run -v ${PWD}:/data boutroslab/cld_docker cld --task=make_database --output-dir=/data --organism arabidopsis_thaliana --rsync-link=rsync://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/current/
Possible precedence issue with control flow operator at /usr/local/share/perl/5.26.1/Bio/DB/IndexedBase.pm line 845.
arabidopsis_thaliana
rsync: failed to connect to ftp.ensemblgenomes.ebi.ac.uk (193.62.193.141): Connection refused (111)
rsync error: error in socket IO (code 10) at clientserver.c(125) [Receiver=3.1.2]

There was some problem with the rsync connection to ensembl.
Maybe you have a typo in the server address or some proxy is hindering the access.

PS: This (ftp.ensemblgenomes.org/all/pub/plants/current/) one does't work anymore, so I used this one .

--rsync-link=<rsync://path/to/dir>           Specify an ftp repository to build the database from.
                                    it must be one of the organisms available in ENSEMBLs ftp repository.
                                    And in the same format as its ENSEMBL rsync directoy path.
                                    E.g.:
                                    rsync://ftp.ensembl.org/ensembl/pub/release-106/

                                    rsync://ftp.ensemblgenomes.org/all/pub/protists/current/
                                    rsync://ftp.ensemblgenomes.org/all/pub/plants/current/