Difference between revisions of "ChlamDB"

Revision as of 17:23, 6 November 2018

Mise en ligne de la base de donnée Chlamdb

Page d’accueil

mettre un nouvel onglet avec qq infos
écrire une page tuto avec fonctions de base
exporter le fichier avec environnementale conda nécessaire pour faire tourner la base de donnée

Setup chlamdb

old setup

new setup

Setup environnement fonctionnel

Conda

name: chlamdb
channels:
 - r
 - etetoolkit
 - bioconda
 - conda-forge
 - defaults
dependencies:
 - python=3.5.6
 - django=2.1.1
 - django-extensions
 - bibtexparser
 - cairo
 - r-cairo
 - r-vegan
 - r-gplots
 - r-gdtools
 - r-svglite
 - pandas
 - qtconsole
 - ete3
 - ete_toolchain
 - pyqt=4.11.4
 - matplotlib
 - scipy
 - pylibmc
 - simplejson
 - dill
 - gunicorn
 - numpy 
 - pyqt 
 - lxml 
 - conda-build
 - reportlab
 - biopython
 - django-crispy-forms
 - mysqlclient
 - pip:
   - cython
   - django-citations

packages R absents de conda à installer à la main

- genoPlotR - flextable

setup X server pour ete3

1apt-get install  xserver-xorg xdm  xfonts-base xfonts-100dpi xfonts-75dpi

1In our example, edit the /etc/X11/xdm/xdm-config file and set following values:
2
3DisplayManager*authorize:       false
4DisplayManager*authComplain:    false

1/etc/init.d/xdm restart

1export DISPLAY=':0'

setup https

setup certificate and key with letsencrypt

1systemctl stop nginx
2letsencrypt certonly
3systemctl start nginx

update config

 1upstream monsite {
 2    # Adresse du serveur wsgi, par exemple gunicorn
 3        server localhost:8001;
 4        }
 5
 6# HTTP Request will be Redirected to the HTTPS
 7server {
 8      listen 80;
 9      server_name chlamdb.ch;
10      return 301 https://$server_name$request_uri;
11      }
12
13server {
14    listen 443 ssl;
15    server_name chlamdb.ch;
16    
17    ssl_certificate /etc/letsencrypt/live/chlamdb.ch/fullchain.pem;
18    ssl_certificate_key /etc/letsencrypt/live/chlamdb.ch/privkey.pem;
19    
20    access_log /webapps/logs/GEN.access.log;
21    error_log /webapps/logs/GEN.error.log;
22    
23    location / {
24        #include fastcgi_params;
25        proxy_pass http://monsite;
26        proxy_redirect off;
27        proxy_set_header Host $http_host;
28        proxy_set_header X-Real-IP $remote_addr;
29        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
30        proxy_set_header X-Forwarded-Proto $scheme;
31    }
32
33    location /assets {
34        autoindex on;
35        alias /home/ubuntu/dev/chlamdb/assets/;
36    }
37}

Difference between revisions of "ChlamDB"

Revision as of 17:23, 6 November 2018

Contents

Mise en ligne de la base de donnée Chlamdb

Page d’accueil

Setup chlamdb

Setup environnement fonctionnel

Conda

packages R absents de conda à installer à la main

setup X server pour ete3

setup https

setup certificate and key with letsencrypt

update config

Navigation menu

Search

@@ Line 25: / Line 25: @@
   name: chlamdb
   channels:
-   - anaconda
+   - r
    - etetoolkit
    - bioconda
    - conda-forge
-  - r
    - defaults
   dependencies:
-   - pyqt=4.11.4=py35_4
+   - python=3.5.6
-  - reportlab=3.4.0=py35_0
+   - django=2.1.1
-  - sip=4.18=py35_0
+   - django-extensions
-  - blast=2.6.0=boost1.60_0
+   - bibtexparser
-   - circos=0.69.6=1
+   - cairo
-  - perl-carp=1.38=pl526_1
+   - r-cairo
-  - perl-clone=0.38=pl526_1
+   - r-vegan
-  - perl-config-general=2.61=pl526_1
+   - r-gplots
-  - perl-data-dumper=2.161=pl526_2
+   - r-gdtools
-  - perl-digest-perl-md5=1.9=pl526_1
+   - r-svglite
-  - perl-encode=2.88=pl526_1
+   - pandas
-  - perl-exporter=5.72=pl526_1
+   - qtconsole
-  - perl-exporter-tiny=1.000000=pl526_0
+   - ete3
-  - perl-extutils-makemaker=7.34=pl526_2
+   - ete_toolchain
-  - perl-font-ttf=1.06=pl526_0
+   - pyqt=4.11.4
-  - perl-gd=2.68=pl526he941832_0
+   - matplotlib
-  - perl-io-string=1.08=pl526_3
+   - scipy
-  - perl-list-moreutils=0.428=pl526_1
+   - pylibmc
-  - perl-list-moreutils-xs=0.428=pl526_0
+   - simplejson
-  - perl-math-bezier=0.01=pl526_1
+   - dill
-  - perl-math-round=0.07=pl526_1
+   - gunicorn
-  - perl-math-vecstat=0.08=pl526_1
+   - numpy
-  - perl-module-implementation=0.09=pl526_2
+   - pyqt
-  - perl-module-runtime=0.016=pl526_0
+   - lxml
-  - perl-number-format=1.75=pl526_2
+   - conda-build
-  - perl-params-validate=1.26=pl526_1
+   - reportlab
-  - perl-parent=0.236=pl526_1
+   - biopython
-  - perl-pathtools=3.73=h470a237_2
+   - django-crispy-forms
-  - perl-readonly=1.04=pl526_2
+   - mysqlclient
-  - perl-regexp-common=2017060201=pl526_0
-  - perl-scalar-list-utils=1.45=pl526h470a237_3
-  - perl-set-intspan=1.19=pl526_1
-  - perl-statistics-basic=1.6611=pl526_2
-  - perl-svg=2.64=pl526_2
-  - perl-test-more=1.001002=pl526_1
-  - perl-text-format=0.59=pl526_1
-  - perl-time-hires=1.9758=pl526_0
-  - perl-try-tiny=0.24=pl526_3
-  - perl-xml-parser=2.44=pl526h3a4f0e9_6
-  - perl-xsloader=0.24=pl526_0
-  - bibtexparser=1.0.1=py_1
-  - ca-certificates=2018.8.13=ha4d7672_0
-   - django-extensions=2.0.7=py_0
-   - freetype=2.8.1=hfa320df_1
-   - jpeg=9c=h470a237_0
-  - krb5=1.14.6=0
-  - libgd=2.2.5=3
-  - libgfortran=3.0.0=1
-  - libmemcached=1.0.18=hc46c6b1_1
-  - libwebp=0.5.2=7
-  - pango=1.40.14=0
-  - pylibmc=1.5.2=py35h470a237_1
-   - r-assertthat=0.2.0=r3.4.1_0
-   - r-base=3.4.1=h4fe35fd_8
-   - r-bh=1.66.0_1=r3.4.1_0
-  - r-bindr=0.1.1=r3.4.1_0
-  - r-bindrcpp=0.2.2=r341h9d2a408_0
-  - r-bit=1.1_12=r341h470a237_1
-  - r-bit64=0.9_5=r341h470a237_1
-  - r-blob=1.1.1=r3.4.1_0
-  - r-cli=1.0.0=r3.4.1_0
-  - r-cluster=2.0.6=r3.4.1_0
-  - r-colorspace=1.3_2=r341h470a237_1
-  - r-crayon=1.3.4=r3.4.1_0
-  - r-dbi=1.0.0=r341_0
-  - r-dbplyr=1.2.2=r341_0
-  - r-dichromat=2.0_0=r3.4.1_0
-  - r-digest=0.6.15=r341h470a237_1
-  - r-dplyr=0.7.6=r341h9d2a408_0
-   - r-gdtools=0.1.6=r341h25a8765_1
-  - r-ggplot2=3.0.0=r341h6115d3f_0
-  - r-glue=1.3.0=r341h470a237_1
-  - r-gtable=0.2.0=r3.4.1_0
-  - r-labeling=0.3=r3.4.1_0
-  - r-lattice=0.20_34=r3.4.1_0
-  - r-lazyeval=0.2.1=r341h470a237_1
-  - r-magrittr=1.5=r3.4.1_0
-  - r-mass=7.3_50=r341hc070d10_1
-  - r-matrix=1.2_14=r341h470a237_1
-  - r-memoise=1.1.0=r3.4.1_0
-  - r-mgcv=1.8_24=r341h470a237_1
-  - r-munsell=0.5.0=r341_0
-  - r-nlme=3.1_131=r341ha44fe06_1
-  - r-permute=0.9_4=r3.4.1_1
-  - r-pillar=1.2.2=r341h6115d3f_1
-  - r-pkgconfig=2.0.2=r341_0
-  - r-plogr=0.2.0=r341h6115d3f_0
-  - r-plyr=1.8.4=r341hfc679d8_1
-  - r-prettyunits=1.0.2=r3.4.1_0
-  - r-purrr=0.2.5=r341h470a237_0
-  - r-r6=2.2.2=r3.4.1_0
-  - r-rcolorbrewer=1.1_2=r3.4.1_0
-  - r-rcpp=0.12.17=r341h9d2a408_1
-  - r-reshape2=1.4.3=r341hfc679d8_1
-  - r-rlang=0.2.1=r341h470a237_1
-  - r-rsqlite=2.0=r341hfc679d8_1
-  - r-scales=1.0.0=r341hfc679d8_0
-  - r-stringi=1.2.3=r341hfc679d8_1
-  - r-stringr=1.3.1=r341_0
-   - r-svglite=1.2.1=r3.4.1_0
-   - r-tibble=1.4.2=r341h470a237_1
-   - r-tidyselect=0.2.4=r341hfc679d8_1
-   - r-utf8=1.1.3=r341h470a237_1
-   - r-vegan=2.4_3=r3.4.1_0
-   - r-viridislite=0.3.0=r3.4.1_0
-  - r-withr=2.1.1=r3.4.1_0
-  - rpy2=2.9.4=py35r341h24bf2e0_0
-  - tk=8.6.8=0
-  - xorg-kbproto=1.0.7=h470a237_2
-  - xorg-libice=1.0.9=h470a237_4
-  - xorg-libsm=1.2.2=h470a237_5
-  - xorg-libx11=1.6.6=h470a237_0
-  - xorg-libxau=1.0.8=h470a237_6
-  - xorg-libxdmcp=1.1.2=h470a237_7
-  - xorg-libxext=1.3.3=h470a237_4
-  - xorg-libxrender=0.9.10=h470a237_2
-  - xorg-libxt=1.1.5=h470a237_2
-  - xorg-renderproto=0.11.1=h470a237_2
-  - xorg-xextproto=7.3.0=h470a237_2
-  - xorg-xproto=7.0.31=h470a237_7
-  - asn1crypto=0.24.0=py35_0
-  - backcall=0.1.0=py35_0
-  - beautifulsoup4=4.6.3=py35_0
-   - binutils_impl_linux-64=2.31.1=h6176602_1
-   - binutils_linux-64=2.31.1=h6176602_2
-   - biopython=1.72=py35h04863e7_0
-   - blas=1.0=mkl
-   - boost=1.60.0=py35_0
-   - bzip2=1.0.6=h14c3975_5
-   - cairo=1.14.12=h7636065_2
-   - certifi=2018.8.24=py35_1
-   - cffi=1.11.5=py35h9745a5d_0
-  - chardet=3.0.4=py35hb6e9ddf_1
-  - click=6.7=py35h353a69f_0
-  - conda=4.5.10=py35_0
-   - conda-build=3.13.0=py35_0
-   - conda-env=2.6.0=1
-   - conda-verify=3.1.0=py35_0
-  - cryptography=2.3=py35hb7f436b_0
-  - cryptography-vectors=2.3=py35_0
-  - curl=7.61.0=h84994c4_0
-  - cycler=0.10.0=py35hc4d5149_0
-  - dbus=1.13.2=h714fa37_1
-  - decorator=4.3.0=py35_0
-  - dill=0.2.8.2=py35_0
-   - django=2.1=py35_0
-  - expat=2.2.5=he0dffb1_0
-  - filelock=3.0.4=py35_0
-  - fontconfig=2.12.6=h49f89f6_0
-  - fribidi=1.0.4=h14c3975_0
-  - future=0.16.0=py35_1
-  - gcc_impl_linux-64=7.3.0=habb00fd_1
-  - gcc_linux-64=7.3.0=h553295d_2
-  - gfortran_impl_linux-64=7.3.0=hdf63c60_1
-  - gfortran_linux-64=7.3.0=h553295d_2
-  - giflib=5.1.4=h14c3975_1
-  - glib=2.56.1=h000015b_0
-  - glob2=0.6=py35hff66265_0
-  - graphite2=1.3.11=h16798f4_2
-  - gsl=2.2.1=h0c605f7_3
-  - gst-plugins-base=1.14.0=hbbd80ab_1
-  - gstreamer=1.14.0=hb453b48_1
-  - gunicorn=19.9.0=py35_0
-  - gxx_impl_linux-64=7.3.0=hdf63c60_1
-  - gxx_linux-64=7.3.0=h553295d_2
-  - harfbuzz=1.7.6=h5f0a787_1
-  - icu=58.2=h9c2bf20_1
-  - idna=2.7=py35_0
-  - intel-openmp=2018.0.3=0
-  - ipykernel=4.8.2=py35_0
-  - ipython=6.5.0=py35_0
-  - ipython_genutils=0.2.0=py35hc9e07d0_0
-  - jedi=0.12.1=py35_0
-  - jinja2=2.10=py35h480ab6d_0
-  - jupyter_client=5.2.3=py35_0
-  - jupyter_core=4.4.0=py35ha89e94b_0
-  - libcurl=7.61.0=h1ad7b7a_0
-  - libedit=3.1.20170329=h6b74fdf_2
-  - libffi=3.2.1=hd88cf55_4
-  - libgcc=7.2.0=h69d50b8_2
-  - libgcc-ng=8.2.0=hdf63c60_1
-  - libgfortran-ng=7.3.0=hdf63c60_0
-  - libiconv=1.15=h63c8f33_5
-  - libopenblas=0.3.2=h9ac9557_0
-  - libpng=1.6.34=hb9fc6fc_0
-  - libsodium=1.0.16=h1bed415_0
-  - libssh2=1.8.0=h9cfc8f7_4
-  - libstdcxx-ng=8.2.0=hdf63c60_1
-  - libtiff=4.0.9=he85c1e1_1
-  - libuuid=1.0.3=h1bed415_2
-  - libxcb=1.13=h1bed415_1
-  - libxml2=2.9.8=h26e45fe_1
-  - libxslt=1.1.32=h1312cb7_0
-  - lxml=4.2.4=py35hf71bdeb_0
-  - make=4.2.1=h1bed415_1
-  - markupsafe=1.0=py35h4f4fcf6_1
-  - matplotlib=1.5.1=np111py35_0
-  - mkl=2018.0.3=1
-  - mkl_fft=1.0.4=py35h4414c95_1
-  - mkl_random=1.0.1=py35h629b387_0
-  - mysql-connector-c=6.1.11=hf4847fb_0
-   - mysqlclient=1.3.13=py35h14c3975_0
-  - ncurses=6.1=hf484d3e_0
-  - numpy=1.15.0=py35h1b885b7_0
-  - numpy-base=1.15.0=py35h3dfced4_0
-  - olefile=0.45.1=py35_0
-  - openssl=1.0.2p=h14c3975_0
-  - pandas=0.23.4=py35h04863e7_0
-  - parso=0.3.1=py35_0
-  - patchelf=0.9=hf484d3e_2
-  - pcre=8.42=h439df22_0
-  - perl=5.26.2=h14c3975_0
-  - pexpect=4.6.0=py35_0
-  - pickleshare=0.7.4=py35hd57304d_0
-  - pillow=5.1.0=py35h3deb7b8_0
-  - pip=10.0.1=py35_0
-  - pixman=0.34.0=hceecf20_3
-  - pkginfo=1.4.2=py35_1
-  - prompt_toolkit=1.0.15=py35hc09de7a_0
-  - psutil=5.4.7=py35h14c3975_0
-  - ptyprocess=0.6.0=py35_0
-  - pycosat=0.6.3=py35h6b6bb97_0
-  - pycparser=2.18=py35h61b3040_1
-  - pygments=2.2.0=py35h0f41973_0
-  - pyopenssl=18.0.0=py35_0
-  - pyparsing=2.2.0=py35h041ed72_1
-  - pysocks=1.6.8=py35_0
-  - python=3.5.5=hc3d631a_4
-  - python-dateutil=2.7.3=py35_0
-  - pytz=2018.5=py35_0
-  - pyyaml=3.13=py35h14c3975_0
-  - pyzmq=17.1.2=py35h14c3975_0
-  - qt=4.8.7=4
-  - qtconsole=4.3.1=py35h4626a06_0
-  - readline=7.0=ha6073c6_4
-  - requests=2.19.1=py35_0
-  - ruamel_yaml=0.15.46=py35h14c3975_0
-  - scipy=1.1.0=py35hfc37229_0
-  - setuptools=40.0.0=py35_0
-  - simplegeneric=0.8.1=py35_2
-  - simplejson=3.16.0=py35h14c3975_0
-  - six=1.11.0=py35h423b573_1
-  - sqlite=3.24.0=h84994c4_0
-  - tornado=5.1=py35h14c3975_0
-  - traitlets=4.3.2=py35ha522a97_0
-  - typing=3.6.4=py35_0
-  - tzlocal=1.5.1=py35_0
-  - urllib3=1.23=py35_0
-  - wcwidth=0.1.7=py35hcd08066_0
-  - wheel=0.31.1=py35_0
-  - xz=5.2.4=h14c3975_4
-  - yaml=0.1.7=had09818_2
-  - zeromq=4.2.5=hf484d3e_0
-  - zlib=1.2.11=ha838bed_2
-  - argtable2=2.13=0
-  - clustalo=1.2.4=h4346872_0
-  - dialigntx=1.0.2=hdce4c0c_0
-  - ete2=2.3.10=py_0
-  - ete3=3.0.0b36=py_0
-  - ete_toolchain=3.0.0=h73706c9_0
-  - fasttree=2.1=hdfd2403_0
-  - iqtree=1.5.5=he390d98_0
-  - kalign=2.03=h29c49b8_0
-  - mafft=6.861=h7f9ae3c_0
-  - muscle=3.8.31=he5e28f3_0
-  - paml=4.8=h48adae2_0
-  - phylobayes=4.1c=hac87e47_0
-  - phyml=20160115.patched=hee5dff1_0
-  - pmodeltest=1.4=py35h5f63f2b_0
-  - raxml=8.2.11=h6db2ed4_0
-  - slr=1.4.3=h69822e3_0
-  - t_coffee=11.00=h99d273f_0
-  - trimal=1.4=h87cb4c3_0
-  - _r-mutex=1.0.0=mro_2
-  - r-bitops=1.0_6=r3.4.1_2
-  - r-cairo=1.5_9=r3.4.1_1
-  - r-catools=1.17.1=r3.4.1_2
-  - r-gdata=2.18.0=r3.4.1_0
-  - r-gplots=3.0.1=r3.4.1_0
-  - r-gtools=3.5.0=r3.4.1_0
-  - r-kernsmooth=2.23_15=r3.4.1_0
    - pip:
-     - cython==0.28.5
+     - cython
-     - django-citations==0.3
+     - django-citations
 ==== packages R absents de conda à installer à la main ====