search

carp-te / carp-documentation

Other
1 stars 1 forks source link

clarify RepBase as a directory #22

Closed luzengAdelaide closed 6 years ago

luzengAdelaide commented 6 years ago

@kortschak @dadelson Can you please help me to take a look and merge it? Many thanks, Lu

kortschak commented 6 years ago

Is this based on a report? I don't see the need for this, though the /home/a.../ should be replaced with ~/.

luzengAdelaide commented 6 years ago

@kortschak Yes, it's for the report. I should change the /home/a.../ with ~/. Should we close this merge, and open a new branch to change?

kortschak commented 6 years ago

What was the complaint? I don't understand.

luzengAdelaide commented 6 years ago

The issue is the name of "RepBase20.04.fasta" in Java code may cause confusing. It's a directory that stores Repbase libraries, rather a fasta sequence, so I'm thinking to make it more clearer.

kortschak commented 6 years ago

OK, but has someone actually had that confusion and filed an issue offline (obviously not here)?

The current text is /home/aXXXXXX/RepBase20.04.fasta/*rep.ref which makes it clear that "RepBase20.04.fasta" is a directory (the trailing/ gives us that).

luzengAdelaide commented 6 years ago

OK, you're right. So I won't change the "/home/aXXXXXX/RepBase20.04.fasta/*rep.ref", but I may clarify RepBase20.04.fasta is a directory in the brackets. Should I close this merge, and open a new branch to remove /home/aXXXXXX/?

kortschak commented 6 years ago

Yes, close this. Fix the hard coded paths (check elsewhere for this as well), and maybe add a note that "Repeat library files are kept in the 'RepBase20.04.fasta' directory." I don't really think it's necessary, but if it makes you feel better, add some text like that.