Mosaic CLI v0.9.4 (Linux x64)

Adds a new -c or --config option to mosaic post, mosaic init, and mosaic experiment.

Using a config file

Instead of using environment variables, some commands offer the option of using the -c or --config option. With this option you will pass a filename
of a config file instead of using environment variables. For example, you could have a file config.txt that looks like the following:

MOSAIC_URL=https://0.0.0.0:3000/
MOSAIC_USERNAME=slichtenberg@frameshift.io
MOSAIC_PASSWORD=my$password

Then when calling MosaicCLI you use the following options:

$ mosaic init -c config.txt my_project
project_id 2

Mosaic CLI v0.9.3 (Linux x64)

Fixes a typo in the success message when POSTing back to Mosaic

Mosaic CLI v0.9.2 (Linux x64)

Adds unsupported as a reference type for mosaic init, mosaic bam, and mosaic vcf. This should be used for projects where Mosaic does not yet support the reference. Note that many functions of Mosaic will not work in a project with an unsupported reference.

Mosaic CLI v0.9.1 (Linux x64)

Adds a -x or --experiment-id to mosaic post. Adding this option will make it so all the files in the gathered JSON file will be added to the specified experiment. This can be used in place of the -x option in mosaic bam and mosaic vcf. If the -x option was used in mosaic bam or mosaic vcf, the -x option in mosaic post will overwrite it.

Mosaic CLI v0.9.0 (Linux x64)

Adds a new command, mosaic experiment. This lets users create experiments and will return the ID of the created experiment. This can be used in conjunction with the -x parameters for mosaic bam and mosaic vcf. For example:

EXP_ID=$(mosaic experiment 1 test-experiment | cut -d ' ' -f 2)
mosaic bam -x $EXP_ID sample_id bam_url

Mosaic CLI v0.8.7 (Linux x64)

Adds a -S or --samples-file tag to mosaic vcf to allow the user to pass a samples file in the format in the BCFtools docs http://samtools.github.io/bcftools/bcftools.html

Mosaic CLI v0.8.6 (Linux x64)

mosaic bam, mosaic vcf, and mosaic vcf now support GRCz11 and GRCm39 as options for the -r flag. Additionally, instead of using 37 and 38, the user should instead use GRCh37 and GRCh38 for the flag, however 37 and 38 will still be supported.

Mosaic CLI v0.8.5 (Linux x64)

mosaic bam and mosaic vcf now have a -x or --experiment-id option where you can pass an experiment ID for which the files will belong to. Then when you gather and post Mosaic will attach these files to the correct experiment.

Also, mosaic post now has a -o or --overwrite-existing flag which defaults to false, but if set to true will overwrite the sample's file with the new files. By default, the files just get appended to the sample.

Mosaic CLI v0.8.4 (Linux x64)

mosaic post now takes in a -e or --endpoint-url parameter. This is needed when using S3 Compatible Object Storage and will now allow Mosaic to work properly with these types of files when the -e parameter is used.

Mosaic CLI v0.8.3 (Linux x64)

Now when using mosaic post you can add a -i flag which will attach the AWS credentials in the request back to Mosaic. Unless the user has already registered credentials for the bucket with Mosaic, this param will be required for the data to be processed if the files are on S3.

This option requires that the credentials are valid for all buckets in a gathered file. If you have multiple sets of credentials for different buckets, then you should process and POST each set of data separately.