Commit 75e0e351 authored by Mathieu Giraud's avatar Mathieu Giraud

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

Closes #3003.
parent f2f25ce8
...@@ -3,8 +3,8 @@ ...@@ -3,8 +3,8 @@
** Algorithm -- Installation instructions ** Algorithm -- Installation instructions
#+BEGIN_SRC sh #+BEGIN_SRC sh
make ; make germline ; make data make
./vidjil -h ./vidjil-algo -h
#+END_SRC #+END_SRC
Detailed compilation, installation and usage instructions Detailed compilation, installation and usage instructions
......
...@@ -159,11 +159,15 @@ Xcode should be installed first. ...@@ -159,11 +159,15 @@ Xcode should be installed first.
** Installation ** Installation
*** Compiling *** 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 #+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: # get IMGT germline databases (IMGT/GENE-DB) -- you have to agree to IMGT license:
# academic research only, provided that it is referred to IMGT®, # academic research only, provided that it is referred to IMGT®,
# and cited as "IMGT®, the international ImMunoGeneTics information system® # and cited as "IMGT®, the international ImMunoGeneTics information system®
...@@ -173,10 +177,10 @@ make germline ...@@ -173,10 +177,10 @@ make germline
# either # either
make # build Vijil from the sources (see the requirements, above) make -C src # build Vijil from the sources (see the requirements, above)
# or # 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) # download a static binary (built for x86_64 architectures)
./vidjil-algo -h # display help/usage ./vidjil-algo -h # display help/usage
...@@ -207,13 +211,13 @@ apt-get install vidjil ...@@ -207,13 +211,13 @@ apt-get install vidjil
You can run the tests with the following commands: You can run the tests with the following commands:
#+BEGIN_SRC sh #+BEGIN_SRC sh
make data make -C src/tests/data
# get IGH recombinations from a single individual, as described in: # get IGH recombinations from a single individual, as described in:
# Boyd, S. D., and al. Individual variation in the germline Ig gene # Boyd, S. D., and al. Individual variation in the germline Ig gene
# repertoire inferred from variable region gene rearrangements. J # repertoire inferred from variable region gene rearrangements. J
# Immunol, 184(12), 6986–92. # 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 #+END_SRC
......
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