yum --enablerepo=epel install python2-pip
yum install python-devel
 
pip install -U setuptools
pip install --upgrade pip
pip install tensorflow    もしくは tensorflow-gpu

SpliceAI

本家様 https://github.com/Illumina/SpliceAI

CentOS7でインストールを試みる

yum groupinstall "Development Tools"
yum install zlib-devel bzip2-devel xz-devel curl-devel libyaml-devel

この状態でpip list

Package                      Version
---------------------------- ---------
absl-py                      0.7.1
astor                        0.7.1
backports.ssl-match-hostname 3.5.0.1
backports.weakref            1.0.post1
configobj                    4.7.2
decorator                    3.4.0
enum34                       1.1.6
funcsigs                     1.0.2
futures                      3.2.0
gast                         0.2.2
grpcio                       1.19.0
h5py                         2.9.0
iniparse                     0.4
ipaddress                    1.0.16
Keras-Applications           1.0.7
Keras-Preprocessing          1.0.9
Markdown                     3.1
mock                         2.0.0
numpy                        1.16.2
pbr                          5.1.3
perf                         0.1
pip                          19.0.3
protobuf                     3.7.1
pycurl                       7.19.0
pygobject                    3.22.0
pygpgme                      0.3
pyliblzma                    0.5.3
python-linux-procfs          0.4.9
pyudev                       0.15
pyxattr                      0.5.1
schedutils                   0.4
setuptools                   40.8.0
six                          1.12.0
slip                         0.4.0
slip.dbus                    0.4.0
tensorboard                  1.13.1
tensorflow                   1.13.1
tensorflow-estimator         1.13.0
termcolor                    1.1.0
urlgrabber                   3.10
Werkzeug                     0.15.2
wheel                        0.33.1
yum-metadata-parser          1.1.4
git clone https://github.com/Illumina/SpliceAI
cd SpliceAI
python setup.py install --prefix=/Appl/SpliceAI    *既定は /usr
 
 
[root@ss4 ~]# spliceai --help
Using TensorFlow backend.
usage: spliceai [-h] [-I [I]] [-O [O]] -R R -A A
 
optional arguments:
  -h, --help  show this help message and exit
  -I [I]      path to the input VCF file, defaults to standard in
  -O [O]      path to the output VCF file, defaults to standard out
  -R R        path to the genome fasta file
  -A A        "grch37" (uses GENCODE canonical annotation file in package),
              "grch38" (uses GENCODE canonical annotation file in package), or
              path to a similarly-constructed custom gene annotation file
[root@ss4 ~]#
[root@ss4 ~]# which spliceai
/usr/bin/spliceai
 
[root@ss4 ~]#

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Last-modified: 2019-04-04 (木) 02:03:37 (22d)