Update bootstrap to select between GRCh37/38

[robinandeer]

Latest CCDS is based on GRCh38

[robinandeer]

Links:

• https://s3.eu-central-1.amazonaws.com/chanjo/ccds.15.grch37p13.bed.zip
• https://s3.eu-central-1.amazonaws.com/chanjo/ccds.18.grch38p2.bed.zip

[biocyberman]

Yes, I fumbled for a while with chanjo init and chanjo db setup thinking that I can get the directory ready to work with, but it turns out that chanjo bootstrap does all the work. I don't know when to use the two previous commands then. And also I found that chanjo currently supports only GRCH37. It is may be worth to point that out in the documentation or FAQ. Last but not least, it seems that chanjo developer intends to generate the bed file from CCDS by them self and publish it with chanjo. This is both a good thing and a limiting factor. For example, I don't see a plan to support other organisms of user choices.

[biocyberman]

Okay, maybe I got it after peeking into the code further :)
If I work with GRCh37, I run chanjo bootstrap directly and ignore init, db setup and link commands.

If I work with other genomes, or bed files, I have to through the set of initialization commands, namely init, db setup, link before I can do calculate and other query commands.

I will keep the previous comment to show what a normal user may encounter.