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Switching Vidjil to full https, this line was hard-coded to http

Mikaël Salson authored Sep 22, 2016 and Mathieu Giraud committed Sep 29, 2016

run_copy copied the sequence file into the result file. But the filename used was the internal Web2py filename (which is quite long).
And it was reencoded for the results_file which lead to a very long filename which was likely to exceed the limit of the
filename length.
Now we take the original filename for the data file, which will lead to a much shorter encoded filename

HERBERT Ryan authored Sep 12, 2016 and Mathieu Giraud committed Sep 23, 2016

With the new vidjil packaging, the vidjil executable may not be situated
in the vidjil directory. Therefore it has become necessary to add a
separate DIR_GERMLINE variable to task.py which needs to be added to
defs.py

Mathieu Giraud authored Jul 13, 2016 and Vidjil Team committed Jul 13, 2016

We want to be able to retrieve the last fuses on every sample set

This commit resolves an issue where running a sequence file would not
trigger the fuse on other sample sets.
To achieve this fix, schedule run no longer depends on sample sets and
database calls to fuse are done on each run_fuse

Those files could quickly saturate disk space

Those files could quickly saturate disk space

> pear.py > don't produce output file on failure
> don't reschedule run if pre-process has failed

before > true/false
after > WAIT/QUEUD/RUN/DONE/FAILED

Preprocess filename was an id followed by .fastq. Instead we try to take the
best among the two filenames (or only the first filename, if there is no
second filename). This will be more meaningful to the user and the file
is not necessarily in .fastq format.

The end user should have access to the pre-process log.

There may be pre-processes running on only one file.

Added a parsing of the mixcr assembly report to extract the total number
of reads and add it to the output

This reverts commit c97ab0c531ede8649459168a6cc488a842789d51.
Responsibility for version output has been deferred to the mixcr native
program

Moved some code into fill_field

-t 1 has another meaning for exportClones than for the other
 commands (it is related to stop codons, see:
 https://mixcr.readthedocs.org/en/latest/export.html#command-line-parameters)