rsync -P -avz -e “ssh -p5566 -i /drives/C/Users/Admin/Desktop/cityu_jhli_1.id” /drives/d/Kraken_12.tar.gz cityu_jhli_1@172.16.22.11:/BIGDATA1/cityu_jhli_1/mhyleung/database/findfungi

[Admin.DESKTOP-7JT504C] ➤ scp -P 5566 -i /drives/C/Users/Admin/Desktop/cityu_jhli_1.id -r /drives/d/Kraken_12.tar.gz cityu_jhli_1@172.16.22.11:/BIGDATA1/cityu_jhli_1/mhyleung/database/findfungi

ssh -p5566 -i /drives/C/Users/Admin/Desktop/cityu_jhli_1.id   cityu_jhli_1@172.16.22.11

for line in fhlines:
line = line.strip()
if re.search(“name”, line):
continue
else:
b = []
b = re.split(“\t”,line)
speciesname.append(b[0])
length = len(b)
dic[a[0]][b[0]] = b[length-1]
unique = [unique_speciesname.append(x) for x in speciesname if x not in unique_speciesname]
for sample_name in dic.keys():
samplenames.append(sample_name)
for name in unique_speciesname:
#print name
if dic[sample_name].has_key(name):
print_line = name + “\t” + dic[sample_name][name]
else:
dic[sample_name][name] = “0”
print_line = name + “\t” + dic[sample_name][name]

#print dic
csv_columns = [‘Species’]
for ele in samplenames:
csv_columns.append(ele)
print csv_columns
#csv_columns = [‘No’,’Name’,’Country’]
csv_file = “sample_species.csv”
#{‘SL311014′: {‘Acinetobacter sp. WCHA55′: ‘0.00029’, ‘Streptococcus sp. oral taxon 431′: ‘0.00007’, ‘Bacillus velezensis': ‘0.00001’, ‘Ahniella affigens': ‘0.00003’, ‘Arsenicicoccus sp. oral taxon 190′: ‘0.00077’, ‘Aureimonas sp. AU20′: ‘0’, ‘Mycobacterium sp. MS1601′: ‘0’, ‘Acinetobacter sp. WCHAc010052′: ‘0.00003’, ‘Candidatus Micrarchaeota archaeon Mia14′: ‘0.00000’, ‘Pseudomonas sp. MT-1′: ‘0.00005’, ‘Halothece sp. PCC 7418′: ‘0.00001’}, ‘SL311013′: {‘Acinetobacter sp. WCHA55′: ‘0’, ‘Streptococcus sp. oral taxon 431′: ‘0.00009’, ‘Bacillus velezensis': ‘0.00004’, ‘Candidatus Micrarchaeota archaeon Mia14′: ‘0’, ‘Ahniella affigens': ‘0.00002’, ‘Arsenicicoccus sp. oral taxon 190′: ‘0.00059’, ‘Mycobacterium sp. MS1601′: ‘0.00029’, ‘Acinetobacter sp. WCHAc010052′: ‘0.00001’, ‘Aureimonas sp. AU20′: ‘0.00026’, ‘Pseudomonas sp. MT-1′: ‘0.00003’, ‘Halothece sp. PCC 7418′: ‘0.00001’}, ‘SL311012′: {‘Acinetobacter sp. WCHA55′: ‘0’, ‘Streptococcus sp. oral taxon 431′: ‘0.00008’, ‘Bacillus velezensis': ‘0.00001’, ‘Candidatus Micrarchaeota archaeon Mia14′: ‘0’, ‘Ahniella affigens': ‘0.00001’, ‘Arsenicicoccus sp. oral taxon 190′: ‘0.00054’, ‘Mycobacterium sp. MS1601′: ‘0.00026’, ‘Acinetobacter sp. WCHAc010052′: ‘0.00002’, ‘Aureimonas sp. AU20′: ‘0.00024’, ‘Pseudomonas sp. MT-1′: ‘0.00003’, ‘Halothece sp. PCC 7418′: ‘0.00000’}}
dict_data_mine = []
#dic_ele = {}
for name in unique_speciesname:
dic_ele = {}
dic_ele[“Species”]=name
for key in dic.keys():
#dic_ele[“speciesname”]=>name
dic_ele[key]=dic[key][name]
dict_data_mine.append(dic_ele)
dict_data = [
{‘No': 1, ‘Name': ‘Alex’, ‘Country': ‘India’},
{‘No': 2, ‘Name': ‘Ben’, ‘Country': ‘USA’},
{‘No': 3, ‘Name': ‘Shri Ram’, ‘Country': ‘India’},
{‘No': 4, ‘Name': ‘Smith’, ‘Country': ‘USA’},
{‘No': 5, ‘Name': ‘Yuva Raj’, ‘Country': ‘India’},
]

#print dict_data_mine
try:
with open(csv_file, ‘w’) as csvfile:
writer = csv.DictWriter(csvfile, fieldnames=csv_columns)
writer.writeheader()
for data in dict_data_mine:
writer.writerow(data)
except IOError:
print(“I/O error”)
if __name__== ‘__main__':
main()

root@vm:~# bash <(curl -L -s https://install.direct/go.sh)
Installing V2Ray v4.18.0 on x86_64
Downloading V2Ray: https://github.com/v2ray/v2ray-core/releases/download/v4.18.0/v2ray-linux-64.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   608    0   608    0     0    581      0 --:--:--  0:00:01 --:--:--   581
100 10.5M  100 10.5M    0     0   172k      0  0:01:02  0:01:02 --:--:--  194k
Extracting V2Ray package to /tmp/v2ray.
Archive:  /tmp/v2ray/v2ray.zip
  inflating: /tmp/v2ray/config.json  
   creating: /tmp/v2ray/doc/
  inflating: /tmp/v2ray/doc/readme.md  
  inflating: /tmp/v2ray/geoip.dat    
  inflating: /tmp/v2ray/geosite.dat  
   creating: /tmp/v2ray/systemd/
  inflating: /tmp/v2ray/systemd/v2ray.service  
   creating: /tmp/v2ray/systemv/
  inflating: /tmp/v2ray/systemv/v2ray  
  inflating: /tmp/v2ray/v2ctl        
 extracting: /tmp/v2ray/v2ctl.sig    
  inflating: /tmp/v2ray/v2ray        
 extracting: /tmp/v2ray/v2ray.sig    
  inflating: /tmp/v2ray/vpoint_socks_vmess.json  
  inflating: /tmp/v2ray/vpoint_vmess_freedom.json  
PORT:51332
UUID:7378f6a4-790a-11e9-8f9e-2a86e4085a59
Created symlink /etc/systemd/system/multi-user.target.wants/v2ray.service → /etc/systemd/system/v2ray.service.
V2Ray v4.18.0 is installed.

然后编辑/etc/v2ray/config.json文件，如下设置：

{
  "inbounds": [{
    "port": 10808,  // SOCKS 代理端口，在浏览器中需配置代理并指向这个端口
    "listen": "127.0.0.1",
    "protocol": "socks",
    "settings": {
      "udp": true
    }
  }],
  "outbounds": [{
    "protocol": "vmess",
    "settings": {
      "vnext": [{
        "address": "server", // 服务器地址，请修改为你自己的服务器 ip 或域名
        "port": 10086,  // 服务器端口
        "users": [{ "id": "b831381d-6324-4d53-ad4f-8cda48b30811" }]
      }]
    }
  },{
    "protocol": "freedom",
    "tag": "direct",
    "settings": {}
  }],
  "routing": {
    "domainStrategy": "IPOnDemand",
    "rules": [{
      "type": "field",
      "ip": ["geoip:private"],
      "outboundTag": "direct"
    }]
  }
}

编辑完成后保存，重新启动v2ray

root@vm:~# service v2ray stop
root@vm:~# service v2ray start
root@vm:~# service v2ray status
● v2ray.service - V2Ray Service
   Loaded: loaded (/etc/systemd/system/v2ray.service; enabled; vendor preset: en
   Active: active (running) since Sat 2019-05-18 08:58:43 CST; 5s ago
 Main PID: 8025 (v2ray)
    Tasks: 7 (limit: 2311)
   CGroup: /system.slice/v2ray.service
           └─8025 /usr/bin/v2ray/v2ray -config /etc/v2ray/config.json

5月 18 08:58:43 vm systemd[1]: Started V2Ray Service.
5月 18 08:58:43 vm v2ray[8025]: V2Ray 4.18.0 (Po) 20190228
5月 18 08:58:43 vm v2ray[8025]: A unified platform for anti-censorship.
5月 18 08:58:44 vm v2ray[8025]: 2019/05/18 08:58:44 [Warning] v2ray.com/core: V2

然后Firefox设置代理如下：

设置-常规-网络设置 勾选手动代理配置，在SOCKS主机中填入127.0.0.1本地IP和端口，协议勾选SOCKS_v5 建议勾选使用SOCKSv5时代理DNS

https://github.com/MultiQC

https://github.com/ranger/ranger

https://zhuanlan.zhihu.com/p/34369349

analysis    (noun single  )

analyses (noun)  (multiplex number of analysis)

动词

analyse  a’ n(ə)lʌɪz          发音a 不带鼻音

th 在尾巴 发 f

thanks

中间ch发k的时候要弱化发音

$ git clone git://github.com/kennethreitz/autoenv.git ~/.autoenv

$ echo 'source ~/.autoenv/activate.sh' >> ~/.bashrc

$ cd <path/to/project>

$ touch .env

$ atom .env

export VARIABLE_NAME="value"

 source ~/.bashrc

autoenv: This is the first time you are about to source /path/.env:

autoenv: Are you sure you want to allow this? (y/N)

##########################################

sudo pip install virtualenvwrapper

export WORKON_HOME=~/venvs

source /usr/bin/virtualenvwrapper.sh

mkvirtualenv -p /usr/bin/python3 voseq_environment

[shenzy@LFE0530 VoSeq]$ mkvirtualenv -p /usr/bin/python3 voseq_environment
Running virtualenv with interpreter /usr/bin/python3
Using base prefix '/usr'
New python executable in /home/shenzy/envs/voseq_environment/bin/python3
Also creating executable in /home/shenzy/envs/voseq_environment/bin/python
Installing setuptools, pip, wheel...done.
virtualenvwrapper.user_scripts creating /home/shenzy/envs/voseq_environment/bin/predeactivate
virtualenvwrapper.user_scripts creating /home/shenzy/envs/voseq_environment/bin/postdeactivate
virtualenvwrapper.user_scripts creating /home/shenzy/envs/voseq_environment/bin/preactivate
virtualenvwrapper.user_scripts creating /home/shenzy/envs/voseq_environment/bin/postactivate
virtualenvwrapper.user_scripts creating /home/shenzy/envs/voseq_environment/bin/get_env_details
(voseq_environment) [shenzy@LFE0530 VoSeq]$ workon voseq_environment

pip install django

pip install django-suit

pip install -r requirements.txt

#########################33

cd /home/shenzy/software/VoSeq

workon voseq_environment

source ~/.autoenv/activate.sh      #  使得能够调用 blastn 等 通过  export path

pip install django

pip install django-suit

pip install -r requirements.txt

make serve

(voseq_environment) [shenzy@LFE0530 VoSeq]$ make serve
python voseq/manage.py create_stats –settings=voseq.settings.local
python voseq/manage.py runserver –settings=voseq.settings.local
Performing system checks…

System check identified no issues (0 silenced).
July 16, 2018 – 06:10:13
Django version 1.10.4, using settings ‘voseq.settings.local’
Starting development server at http://127.0.0.1:8000/
Quit the server with CONTROL-C.

(voseq_environment) [shenzy@LFE0530 VoSeq]$ make serve
python voseq/manage.py create_stats –settings=voseq.settings.local
python voseq/manage.py runserver –settings=voseq.settings.local
Performing system checks…

System check identified no issues (0 silenced).
July 16, 2018 – 07:02:22
Django version 1.10.4, using settings ‘voseq.settings.local’
Starting development server at http://127.0.0.1:8000/
Quit the server with CONTROL-C.
^C
(voseq_environment) [shenzy@LFE0530 VoSeq]$ vi setup.py
(voseq_environment) [shenzy@LFE0530 VoSeq]$ vi runserver.py
(voseq_environment) [shenzy@LFE0530 VoSeq]$ python voseq/manage.py runserver –settings=voseq.settings.local 143.89.29.80:8000
Performing system checks…

System check identified no issues (0 silenced).
July 16, 2018 – 07:03:30
Django version 1.10.4, using settings ‘voseq.settings.local’
Starting development server at http://143.89.29.80:8000/

########################

[shenzy@LFE0530 VoSeq]$ sudo -u postgres -i
[postgres@LFE0530 ~]$ psql
psql (9.2.23)
Type “help” for help.

postgres=#

sudo -u postgres -i

 ## Login with postgres user 
sudo -u postgres -i
 export PGDATA=/your_path/data
 pg_ctl -D $PGDATA start &

service postgresql start/status

SHOW data_directory;

postgres=# \q
[postgres@LFE0530 ~]$ pwd
/var/lib/pgsql
[postgres@LFE0530 ~]$ psql
psql (9.2.23)
Type “help” for help.

postgres=# SHOW data_directory;
data_directory
—————-
/home/pgsql
(1 row)

虽然还是显示下面错误，但其实上面的已经可以让 pgsql启动，并服务！！！

Redirecting to /bin/systemctl status postgresql.service
● postgresql.service – PostgreSQL database server
Loaded: loaded (/usr/lib/systemd/system/postgresql.service; disabled; vendor preset: disabled)
Active: failed (Result: exit-code) since 三 2018-07-18 22:31:30 EDT; 5min ago
Process: 8035 ExecStart=/usr/bin/pg_ctl start -D ${PGDATA} -s -o -p ${PGPORT} -w -t 300 (code=exited, status=1/FAILURE)
Process: 8029 ExecStartPre=/usr/bin/postgresql-check-db-dir ${PGDATA} (code=exited, status=0/SUCCESS)

7月 18 22:31:29 LFE0530 pg_ctl[8035]: HINT: Is another postmaster already running on port 5432? If not, wait a few seconds and retry.
7月 18 22:31:29 LFE0530 pg_ctl[8035]: LOG: could not bind IPv4 socket: Address already in use
7月 18 22:31:29 LFE0530 pg_ctl[8035]: HINT: Is another postmaster already running on port 5432? If not, wait a few seconds and retry.
7月 18 22:31:29 LFE0530 pg_ctl[8035]: WARNING: could not create listen socket for “localhost”
7月 18 22:31:29 LFE0530 pg_ctl[8035]: FATAL: could not create any TCP/IP sockets
7月 18 22:31:30 LFE0530 pg_ctl[8035]: pg_ctl: could not start server
7月 18 22:31:30 LFE0530 systemd[1]: postgresql.service: control process exited, code=exited status=1
7月 18 22:31:30 LFE0530 systemd[1]: Failed to start PostgreSQL database server.
7月 18 22:31:30 LFE0530 systemd[1]: Unit postgresql.service entered failed state.
7月 18 22:31:30 LFE0530 systemd[1]: postgresql.service failed.
[root@LFE0530 data]#

voseq=# \COPY public_interface_vouchers(code,notes) FROM ‘/home/shenzy/software/VoSeq/U-RVDBv13.0.voucher_10_5000top.csv’ DELIMITER ‘,’ CSV HEADER;
voseq=#

voseq=#
\COPY public_interface_sequences FROM ‘/home/shenzy/software/VoSeq/all.gene_fasta_10test_import.csv’ DELIMITER ‘,’ CSV;
voseq=#
\COPY public_interface_sequences FROM ‘/home/shenzy/software/VoSeq/all.gene_fasta_10test_import.csv’ DELIMITER ‘,’ CSV;
voseq=#
\COPY public_interface_vouchers FROM ‘/home/shenzy/software/VoSeq/U-RVDBv13.0.voucher_import.csv’ DELIMITER ‘,’ CSV;

###########################
export

voseq=# COPY public_interface_sequences TO ‘/home/shenzy/software/VoSeq/testseq.csv’ WITH CSV;

############33

#empty table
voseq=# truncate table public_interface_sequences  CASCADE;
NOTICE:  truncate cascades to table “public_interface_primers”
TRUNCATE TABLE
voseq=# truncate table public_interface_vouchers CASCADE;
NOTICE:  truncate cascades to table “public_interface_flickrimages”
NOTICE:  truncate cascades to table “public_interface_localimages”
NOTICE:  truncate cascades to table “public_interface_sequences”
NOTICE:  truncate cascades to table “public_interface_primers”

很多人都知道一个下载文献的好地方 Sci-Hub，但是现在 Sci-Hub 的站长 Alexandra Elbakyan 女士面临着爱思唯尔的诉讼，让其面临数百万美元的赔偿。因此现在 Sci-Hub 在某些时候可能不可用了。不过 Alexandra Elbakyan 女士并未妥协，希望大家能多支持一下这位女士（貌似只能接受比特币捐款，我也不知道怎么弄，要是paypal或者payoneer就好了）。

相信很多人都知道下面这两个网址：

Sci-Hub 官网：http://www.sci-hub.org/

Sci-Hub 替代网址：http://www.sci-hub.io/

http://sci-hub.ac/和http://sci-hub.cc/也都已经阵亡（2017月12月6日测试）

以上几个网址都挂了，现在可用的是

http://sci-hub.bz/（12月8日测试 已经不可用了）

http://sci-hub.la/

http://sci-hub.hk/

http://sci-hub.tw/

http://sci-hub.tv/

http://80.82.77.83/

http://80.82.77.84/