-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.txt
181 lines (123 loc) · 5.25 KB
/
README.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
Pygr README
===========
Introduction
------------
Pygr is an open source software project used to develop graph database
interfaces for the popular Python language, with a strong emphasis
on bioinformatics applications ranging from genome-wide analysis of
alternative splicing patterns, to comparative genomics queries of
multi-genome alignment data.
For more information see
http://pygr.org
Latest Release
--------------
http://code.google.com/p/pygr/downloads/list
Documentation
-------------
This distribution includes the full Pygr documentation source,
but you will need the Sphinx documentation tool to build the
formatted docs. You can get Sphinx via:
easy_install -U Sphinx
To build HTML versions of the docs using Sphinx:
cd doc
make html
The docs are also available online:
http://pygr.org/docs/latest-release/
Core Prerequisites
-----------------
1) Python >= 2.3
To build Pygr from source code, you need Pyrex
Apps Prerequiites
-----------------
MySQL-python >= 1.2.0
MySQL >= 3.23.x
Note: While pygr's core functionality is solely dependent on a sane python environment, the aformentioned apps requirements must be installed if one wishes to utilize the apps modules and test code.
Supported Platforms
-------------------
In theory, pygr should work on any platform that adequately supports python.
Here are the OS's we've successfully tested on:
o Linux 2.2.x/2.4.x
o OS X
o OpenBSD
o Windows XP
Installation
------------
Installing pygr is quite simple.
1) tar -xzvf pygr-0.3.tar.gz
2) cd pygr
3) python setup.py install
Once the test framework has completed successfully, the setup script
will install pygr into python's respective site-packages directory.
If you don't want to install pygr into your system-wide site-packages,
replace the "python setup.py install" command with
"python setup.py build". This will build pygr but not install it
in site-packages.
IGB Installation -- CentOS 5 and 6, python 2.6
==============================================
Ensure that you have sourced the ${MOTIFMAP_ENV}/profile before
proceeding. This should point to the absolute path of the
motifmap-devel checkout
To compile, issue the following command
LDFLAGS="-L${MOTIFMAP_ENV}/lib64" python setup.py build
Pyrex warnings are normal and should compile to completion if you
are using gcc 4.1.2. If your system does not have this version,
you will need to update your PATH and LD_LIBRARY_PATH to point
to the gcc/4.1.2 that's shipped with motifmap-devel
export PATH=${MOTIFMAP_ENV}/deps/gcc/4.1.2/bin:$PATH
export LD_LIBRARY_PATH=${MOTIFMAP_ENV}/deps/gcc/4.1.2/lib:$LD_LIBRARY_PATH
To install, issue the following command
LDFLAGS="-L${MOTIFMAP_ENV}/lib64" python setup.py install
This should install the pygr module under
${MOTIFMAP_ENV}/lib64/python2.6/site-packages
IGB Installation -- CentOS 6 and python 2.7
===========================================
Enter the src directory of motifmap-devel
cd codebase/motifmap-devel/src/
If the pygr checkout doesn't exist, make sure to run the pull-submodules.sh
script at the root of the checkout, ie, MOTIFMAP_ENV folder
Now go into the pygr folder and source the latest python 2.7 profile
cd pygr
source /auto/igb-libs/linux/centos/6.x/x86_64/profiles/python_2.7.6
Remove (if necessary) the following files
rm pygr/cdict.c pygr/cnestedlist.c pygr/seqfmt.c
Install correct version of pyrex:
easy_install pyrex==0.9.8.6
Build and install pygr
python setup.py build
python setup.py install
Run the test code at the root of the checkout
python src/pyrexes/pygr-testcode.py
The output should be like the following if the compilation and installation was correct
/auto/igb-libs/linux/centos/6.x/x86_64/pkgs/python/2.7.6/lib/python2.7/site-packages/pygr-0.8.2-py2.7-linux-x86_64.egg/pygr/__init__.pyc
Chrom:chr1, msa: <pygr.nlmsa_utils.EmptySlice instance at 0x26515f0>
Chrom:chr10, msa: <pygr.nlmsa_utils.EmptySlice instance at 0x2651488>
Chrom:chr11, msa: <pygr.nlmsa_utils.EmptySlice instance at 0x7f673dd0f9e0>
Chrom:chr12, msa: <pygr.nlmsa_utils.EmptySlice instance at 0x2651488>
Chrom:chr13, msa: <pygr.nlmsa_utils.EmptySlice instance at 0x7f673dd0f9e0>
Chrom:chr14, msa: <pygr.nlmsa_utils.EmptySlice instance at 0x2651488>
Chrom:chr15, msa: <pygr.nlmsa_utils.EmptySlice instance at 0x7f673dd0f9e0>
... more ...
Chrom:GL172637, msa: <pygr.nlmsa_utils.EmptySlice instance at 0x565b758>
... more ...
Using Pygr
----------
Check out the tutorials in the online docs!
Pygr contains several modules imported as follows:
from pygr import seqdb # IMPORT SEQUENCE DATABASE MODULE
If you did not install pygr in your system-wide site-packages, you
must set your PYTHONPATH to the location of your pygr build.
For example, if your top-level pygr source directory is PYGRDIR then
you'd type something like:
setenv PYTHONPATH PYGRDIR/build/lib.linux-i686-2.3
where the last directory name depends on your specific architecture.
License
-------
New BSD license.
Author
------
Chris Lee <[email protected]> and the rest of the Pygr developer team.
Please see http://code.google.com/p/pygr for a current list
of the participating developers.
Also see http://github.com/cjlee112/pygr/ for a list of other
developers who have created their own branches of the Pygr
git repository.