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INSTALL.org, doc/algo.org: update installation instructions

Closes #3003.
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magiraud committed Jan 29, 2018
1 parent f2f25ce commit 75e0e351caa1fc0889f38e0277f406a24d7cf8d7
Showing with 11 additions and 7 deletions.
  1. +2 −2 INSTALL.org
  2. +9 −5 doc/algo.org
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@@ -3,8 +3,8 @@
** Algorithm -- Installation instructions
#+BEGIN_SRC sh
make ; make germline ; make data
./vidjil -h
make
./vidjil-algo -h
#+END_SRC
Detailed compilation, installation and usage instructions
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@@ -159,11 +159,15 @@ Xcode should be installed first.
** Installation
*** Compiling
Running 'make' from the extracted archive should be enough to install vidjil-algo and run the self-tests (see below).
It runs the commands that are detailed in the following paragraphs.
#+BEGIN_SRC sh
make germline
make -C germline get-saved-data
# get IMGT germline databases (IMGT/GENE-DB) -- you have to agree to IMGT license:
# academic research only, provided that it is referred to IMGT®,
# and cited as "IMGT®, the international ImMunoGeneTics information system®
@@ -173,10 +177,10 @@ make germline
# either
make # build Vijil from the sources (see the requirements, above)
make -C src # build Vijil from the sources (see the requirements, above)
# or
wget http://bioinfo.lifl.fr/vidjil/vidjil-2015.12_x86_64 -O vidjil-algo
wget http://www.vidjil.org/releases/vidjil-latest.tgzvidjil-latest_x86_64 -O vidjil-algo
# download a static binary (built for x86_64 architectures)
./vidjil-algo -h # display help/usage
@@ -207,13 +211,13 @@ apt-get install vidjil
You can run the tests with the following commands:
#+BEGIN_SRC sh
make data
make -C src/tests/data
# get IGH recombinations from a single individual, as described in:
# Boyd, S. D., and al. Individual variation in the germline Ig gene
# repertoire inferred from variable region gene rearrangements. J
# Immunol, 184(12), 6986–92.
make test # run self-tests (can take 5 to 60 minutes)
make -C src test # run self-tests (can take 5 to 60 minutes)
#+END_SRC

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