Submitting results to CAMI
To submit your assembly (or binning, profiling, pathogen detection) result, you first need to generate a fingerprint for your result file using the CAMI client camiClient.jar (more information on the client here). The fingerprint is an alphanumeric code and will be unique for your file. That is, if you modify it, you will need to generate a new fingerprint.
For example, to generate a fingerprint for your assembly, which is stored in myassembly.fasta in this example, use this command (without the $):
$ java -jar camiClient.jar --assemblyFingerprint myassembly.fasta Validation finished Starting to compute fingerprint Use this fingerprint in the cami website: C9E0D1D0936CF82F6937131BD1D44B26160
To generate a fingerprint for binning or profiling results, use the option --binningFingerprint or --profilingFingerprint. In these cases, besides your result file, you need to provide the path to the CAMI 2 taxonomy database for the CAMI client, i.e., the path to the extracted file taxdb.tar.gz. Exemplary sequence of steps:
$ wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/CAMI_DATABASES/taxdb.tar.gz $ tar -xvf taxdb.tar.gz $ java -jar camiClient.jar --profilingFingerprint myresults.profile taxdb
To generate a fingerprint for the clinical pathogen detection results, use the option --clinicalPathologyFingerprint. Note that you can generate a fingerprint for a zip file containing taxa.txt and pathogen.txt.
Next, go to the CAMI website at https://data.cami-challenge.org/participate and login using your account, as shown in the picture:
In the Up- and Download section, go to the dataset that you want to submit your result to, for example the 2nd CAMI Challenge Marine Dataset. Then, click on one of the options: SUBMIT ASSEMBLY or SUBMIT BINNING or SUBMIT PROFILING (or SUBMIT PATHOGEN DETECTION, if applicable):
By clicking, say, on SUBMIT ASSEMBLY, and then on X ASSEMBLY, the following form will open:
Fill out all the information regarding your submission, providing in the Fingerprint* field the fingerprint that you generated as explained above. Note that, while the fields regarding GitHub, Bioconda, release version, etc. are not mandatory, we strongly encourage you to fill them (see our comments on reproducibility of results in the FAQ section). Once you are done, click on SUBMIT. The following message will appear:
Click on GET LINKFILE and save the generated file, preferably in the same directory as your assembly (or binning, or profiling) file. The linkfile is a text file containing the link that is required by the camiClient.jar to upload your file to the CAMI server.
Finally, using the camiClient.jar and the obtained linkfile, upload your file as follows:
$ java -jar camiClient.jar -u linkfile myassembly.fasta