Hi, I'm using the Quick Installation method to show that there is a problem with the python script, should it be python2.7 or python3.5 or above? The command is shown below.Thank you!
Reading package lists... Done
Reading package lists... Done
Building dependency tree
Reading state information... Done
make is already the newest version (4.1-9.1ubuntu1).
python-dev is already the newest version (2.7.15~rc1-1).
python-virtualenv is already the newest version (15.1.0+ds-1.1).
g++ is already the newest version (4:7.4.0-1ubuntu2.3).
gcc is already the newest version (4:7.4.0-1ubuntu2.3).
git is already the newest version (1:2.17.1-1ubuntu0.5).
0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Reading package lists... Done
Building dependency tree
Reading state information... Done
libopenmpi-dev is already the newest version (2.1.1-8).
openmpi-bin is already the newest version (2.1.1-8).
0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Reading package lists... Done
Building dependency tree
Reading state information... Done
hmmer2 is already the newest version (2.3.2+dfsg-5).
0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Cloning into 'galaxy'...
remote: Enumerating objects: 23, done.
remote: Counting objects: 100% (23/23), done.
remote: Compressing objects: 100% (20/20), done.
remote: Total 428021 (delta 2), reused 7 (delta 2), pack-reused 427998
Receiving objects: 100% (428021/428021), 484.83 MiB | 18.45 MiB/s, done.
Resolving deltas: 100% (339178/339178), done.
Checking out files: 100% (4997/4997), done.
Reading package lists... Done
Building dependency tree
Reading state information... Done
emboss is already the newest version (6.6.0+dfsg-6build1).
hmmer is already the newest version (3.1b2+dfsg-5ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
created virtual environment CPython3.7.0.final.0-64 in 553ms
creator CPython3Posix(dest=/root/mgescan3/virtualenv/mgescan, clear=False, global=False)
seeder FromAppData(download=False, pip=latest, setuptools=latest, wheel=latest, via=copy, app_data_dir=/root/.local/share/virtualenv/seed-v1)
activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
--2020-02-25 08:41:41-- http://tandem.bu.edu/trf/downloads/trf407b.linux64
Resolving tandem.bu.edu (tandem.bu.edu)... 128.197.114.130
Connecting to tandem.bu.edu (tandem.bu.edu)|128.197.114.130|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 111670 (109K) [application/octet-stream]
Saving to: ‘/root/mgescan3/trf/trf407b.linux64’
trf407b.linux64 100%[====================================================>] 109.05K --.-KB/s in 0.06s
root@vultr:~/MGEScan1.3.1/MGEScan_nonLTR_v2/resultnonltr# curl -L https://raw.githubusercontent.com/MGEScan/mgescan/master/one-liner/ubuntu | bash % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1272 100 1272 0 0 9709 0 --:--:-- --:--:-- --:--:-- 9709 Get:1 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB] Hit:2 https://packages.microsoft.com/repos/vscode stable InRelease Hit:3 http://archive.ubuntu.com/ubuntu bionic InRelease Get:4 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB] Get:5 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB] Get:6 http://security.ubuntu.com/ubuntu bionic-security/main amd64 Packages [651 kB] Get:7 http://security.ubuntu.com/ubuntu bionic-security/main i386 Packages [442 kB] Get:8 http://security.ubuntu.com/ubuntu bionic-security/main Translation-en [211 kB] Get:9 http://security.ubuntu.com/ubuntu bionic-security/universe i386 Packages [617 kB] Get:10 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages [649 kB] Get:11 http://security.ubuntu.com/ubuntu bionic-security/universe Translation-en [218 kB] Get:12 http://security.ubuntu.com/ubuntu bionic-security/multiverse amd64 Packages [6,760 B] Get:13 http://security.ubuntu.com/ubuntu bionic-security/multiverse Translation-en [2,700 B] Get:14 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 Packages [871 kB] Get:15 http://archive.ubuntu.com/ubuntu bionic-updates/main i386 Packages [650 kB] Get:16 http://archive.ubuntu.com/ubuntu bionic-updates/main Translation-en [303 kB] Get:17 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages [1,054 kB] Get:18 http://archive.ubuntu.com/ubuntu bionic-updates/universe i386 Packages [1,010 kB] Get:19 http://archive.ubuntu.com/ubuntu bionic-updates/universe Translation-en [326 kB] Get:20 http://archive.ubuntu.com/ubuntu bionic-updates/multiverse amd64 Packages [10.1 kB] Get:21 http://archive.ubuntu.com/ubuntu bionic-updates/multiverse Translation-en [4,636 B] Fetched 7,278 kB in 5s (1,411 kB/s)
Reading package lists... Done Reading package lists... Done Building dependency tree Reading state information... Done make is already the newest version (4.1-9.1ubuntu1). python-dev is already the newest version (2.7.15~rc1-1). python-virtualenv is already the newest version (15.1.0+ds-1.1). g++ is already the newest version (4:7.4.0-1ubuntu2.3). gcc is already the newest version (4:7.4.0-1ubuntu2.3). git is already the newest version (1:2.17.1-1ubuntu0.5). 0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded. Reading package lists... Done Building dependency tree Reading state information... Done libopenmpi-dev is already the newest version (2.1.1-8). openmpi-bin is already the newest version (2.1.1-8). 0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded. Reading package lists... Done Building dependency tree Reading state information... Done hmmer2 is already the newest version (2.3.2+dfsg-5). 0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded. Cloning into 'galaxy'... remote: Enumerating objects: 23, done. remote: Counting objects: 100% (23/23), done. remote: Compressing objects: 100% (20/20), done. remote: Total 428021 (delta 2), reused 7 (delta 2), pack-reused 427998 Receiving objects: 100% (428021/428021), 484.83 MiB | 18.45 MiB/s, done. Resolving deltas: 100% (339178/339178), done. Checking out files: 100% (4997/4997), done. Reading package lists... Done Building dependency tree Reading state information... Done emboss is already the newest version (6.6.0+dfsg-6build1). hmmer is already the newest version (3.1b2+dfsg-5ubuntu1). 0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded. created virtual environment CPython3.7.0.final.0-64 in 553ms creator CPython3Posix(dest=/root/mgescan3/virtualenv/mgescan, clear=False, global=False) seeder FromAppData(download=False, pip=latest, setuptools=latest, wheel=latest, via=copy, app_data_dir=/root/.local/share/virtualenv/seed-v1) activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator --2020-02-25 08:41:41-- http://tandem.bu.edu/trf/downloads/trf407b.linux64 Resolving tandem.bu.edu (tandem.bu.edu)... 128.197.114.130 Connecting to tandem.bu.edu (tandem.bu.edu)|128.197.114.130|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 111670 (109K) [application/octet-stream] Saving to: ‘/root/mgescan3/trf/trf407b.linux64’
trf407b.linux64 100%[====================================================>] 109.05K --.-KB/s in 0.06s
2020-02-25 08:41:42 (1.78 MB/s) - ‘/root/mgescan3/trf/trf407b.linux64’ saved [111670/111670]
Cloning into 'mgescan'... remote: Enumerating objects: 4054, done. remote: Total 4054 (delta 0), reused 0 (delta 0), pack-reused 4054 Receiving objects: 100% (4054/4054), 18.71 MiB | 23.28 MiB/s, done. Resolving deltas: 100% (2619/2619), done. File "setup.py", line 39 os.makedirs(os.environ.get("MGESCAN_SRC"), 0755) ^ SyntaxError: invalid token