Difference between revisions of "ChlamDB"

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 +
==Mise en ligne de la base de donnée Chlamdb==
  
−
== Mise en ligne de la base de donnée Chlamdb ==
 
  
 +
===Page d’accueil===
  
−
=== 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
  
−
* 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===
−
=== Setup chlamdb ===
 
  
 
[[old setup]]
 
[[old setup]]
Line 18: Line 17:
 
[[new setup]]
 
[[new setup]]
  
 +
===Update===
 +
- avril 2019
 +
{| class="wikitable sortable"
 +
|+
 +
!
 +
!N genomes
 +
!N annotated Genbank
 +
!N annotated RS
 +
!N complete genomes
 +
|-
 +
|'''Planctomycetes'''
 +
|600
 +
|423
 +
|60
 +
|20
 +
|-
 +
|'''Chlamydiae'''
 +
|463
 +
|392
 +
|401
 +
|165
 +
|-
 +
|'''Ca. Omnitrophica'''
 +
|172
 +
|137
 +
|4
 +
|0
 +
|-
 +
|'''Kiritimatiellaeota'''
 +
|13
 +
|7
 +
|1
 +
|1
 +
|-
 +
|'''Lentisphaerae'''
 +
|62
 +
|29
 +
|4
 +
|1
 +
|-
 +
|'''Verrucomicrobia'''
 +
|930
 +
|555
 +
|158
 +
|34
 +
|-
 +
|'''TOTAL'''
 +
|'''2249'''
 +
|'''1443'''
 +
|'''628'''
 +
|'''221'''
 +
|}
  
−
=== environnement conda fonctionnel ===
+
===Setup environnement fonctionnel===
  
 +
====Conda====
  
 
  name: chlamdb
 
  name: chlamdb
 
  channels:
 
  channels:
−
   - anaconda
+
   - r
 
   - etetoolkit
 
   - etetoolkit
 
   - bioconda
 
   - bioconda
 
   - conda-forge
 
   - conda-forge
−
  - r
 
 
   - defaults
 
   - defaults
 
  dependencies:
 
  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:
 
   - pip:
−
     - cython==0.28.5
+
     - cython
−
     - django-citations==0.3
+
     - django-citations
  
−
 
+
====packages R absents de conda à installer à la main====
−
=== packages R a installer à la main ===
 
  
 
- genoPlotR
 
- genoPlotR
 
- flextable
 
- flextable
  
−
== setup X server pour ete3 ==
+
====modules python a ajouter à la main====
 +
<syntaxhighlight lang="Bash" line="line">
 +
conda develop /home/ubuntu/dev/orthomcl/
 +
conda develop /home/ubuntu/dev/plots/
 +
conda develop /home/ubuntu/dev/biosqldb/
 +
conda develop /home/ubuntu/dev/utilitaires/
 +
conda develop /home/ubuntu/dev/phylo_tree_display/
 +
conda develop /home/ubuntu/dev/TPutils/
 +
conda develop /home/ubuntu/dev/network_d3/
 +
</syntaxhighlight>
 +
====setup X server pour ete3====
  
−
<syntaxhighlight lang="Bash" line='line'>
+
<syntaxhighlight lang="Bash" line="line">
 
apt-get install  xserver-xorg xdm  xfonts-base xfonts-100dpi xfonts-75dpi
 
apt-get install  xserver-xorg xdm  xfonts-base xfonts-100dpi xfonts-75dpi
 
</syntaxhighlight>
 
</syntaxhighlight>
  
−
<syntaxhighlight lang="Bash" line='line'>
+
<syntaxhighlight lang="Bash" line="line">
 
In our example, edit the /etc/X11/xdm/xdm-config file and set following values:
 
In our example, edit the /etc/X11/xdm/xdm-config file and set following values:
  
Line 335: Line 143:
 
</syntaxhighlight>
 
</syntaxhighlight>
  
−
<syntaxhighlight lang="Bash" line='line'>
+
<syntaxhighlight lang="Bash" line="line">
 
/etc/init.d/xdm restart
 
/etc/init.d/xdm restart
 
</syntaxhighlight>
 
</syntaxhighlight>
  
−
<syntaxhighlight lang="Bash" line='line'>
+
<syntaxhighlight lang="Bash" line="line">
 
export DISPLAY=':0'
 
export DISPLAY=':0'
 +
</syntaxhighlight>
 +
 +
Might be necessary to update the Xservers file as well (/etc/X11/xdm/Xservers)
 +
 +
<syntaxhighlight lang="Bash" line="1">
 +
#:0 local /usr/X11R6/bin/X -dpi 100 -nolisten tcp
 +
:0 local /usr/X11R6/bin/X -dpi 100
 +
</syntaxhighlight>
 +
==setup https==
 +
 +
===setup certificate and key with letsencrypt===
 +
 +
<syntaxhighlight lang="Bash" line="line">
 +
systemctl stop nginx
 +
letsencrypt certonly
 +
systemctl start nginx
 +
</syntaxhighlight>
 +
 +
 +
===update config===
 +
 +
<syntaxhighlight lang="Bash" line="line">
 +
upstream monsite {
 +
    # Adresse du serveur wsgi, par exemple gunicorn
 +
        server localhost:8001;
 +
        }
 +
 +
# HTTP Request will be Redirected to the HTTPS
 +
server {
 +
      listen 80;
 +
      server_name chlamdb.ch;
 +
      return 301 https://$server_name$request_uri;
 +
      }
 +
 +
server {
 +
    listen 443 ssl;
 +
    server_name chlamdb.ch;
 +
   
 +
    ssl_certificate /etc/letsencrypt/live/chlamdb.ch/fullchain.pem;
 +
    ssl_certificate_key /etc/letsencrypt/live/chlamdb.ch/privkey.pem;
 +
   
 +
    access_log /webapps/logs/GEN.access.log;
 +
    error_log /webapps/logs/GEN.error.log;
 +
   
 +
    location / {
 +
        #include fastcgi_params;
 +
        proxy_pass http://monsite;
 +
        proxy_redirect off;
 +
        proxy_set_header Host $http_host;
 +
        proxy_set_header X-Real-IP $remote_addr;
 +
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
 +
        proxy_set_header X-Forwarded-Proto $scheme;
 +
    }
 +
 +
    location /assets {
 +
        autoindex on;
 +
        alias /home/ubuntu/dev/chlamdb/assets/;
 +
    }
 +
}
 +
 +
</syntaxhighlight>
 +
 +
=setup celery=
 +
 +
- install celery, django-celery
 +
- install rabbitmq
 +
<syntaxhighlight lang="Bash" line="line">
 +
sudo apt-get install rabbitmq-server
 +
sudo systemctl enable rabbitmq-server
 +
sudo systemctl start rabbitmq-server
 +
</syntaxhighlight>
 +
 +
- setup user and host
 +
 +
<syntaxhighlight lang="Bash" line="line">
 +
sudo rabbitmqctl add_vhost my_vhost
 +
sudo rabbitmqctl add_user chlamdb estrella3
 +
sudo rabbitmqctl set_permissions -p my_vhost chlamdb "." "." ".*"
 +
</syntaxhighlight>
 +
 +
- launch celery workers
 +
 +
<syntaxhighlight lang="Bash" line="line">
 +
celery -A chlamdb.celeryapp worker -l info
 +
</syntaxhighlight>
 +
 +
 +
=setup on vital-it=
 +
 +
==ete3==
 +
 +
work with the following variable exported:
 +
 +
 +
<syntaxhighlight lang="Bash" line="line">
 +
export QT_QPA_PLATFORM=offscreen
 
</syntaxhighlight>
 
</syntaxhighlight>

Latest revision as of 17:48, 10 March 2020

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

Update

- avril 2019

N genomes N annotated Genbank N annotated RS N complete genomes
Planctomycetes 600 423 60 20
Chlamydiae 463 392 401 165
Ca. Omnitrophica 172 137 4 0
Kiritimatiellaeota 13 7 1 1
Lentisphaerae 62 29 4 1
Verrucomicrobia 930 555 158 34
TOTAL 2249 1443 628 221

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

modules python a ajouter à la main

1conda develop /home/ubuntu/dev/orthomcl/
2conda develop /home/ubuntu/dev/plots/
3conda develop /home/ubuntu/dev/biosqldb/
4conda develop /home/ubuntu/dev/utilitaires/
5conda develop /home/ubuntu/dev/phylo_tree_display/
6conda develop /home/ubuntu/dev/TPutils/
7conda develop /home/ubuntu/dev/network_d3/

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'

Might be necessary to update the Xservers file as well (/etc/X11/xdm/Xservers) 

1#:0 local /usr/X11R6/bin/X -dpi 100 -nolisten tcp
2:0 local /usr/X11R6/bin/X -dpi 100

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}

setup celery

- install celery, django-celery - install rabbitmq 

1sudo apt-get install rabbitmq-server
2sudo systemctl enable rabbitmq-server
3sudo systemctl start rabbitmq-server

- setup user and host 

1sudo rabbitmqctl add_vhost my_vhost
2sudo rabbitmqctl add_user chlamdb estrella3
3sudo rabbitmqctl set_permissions -p my_vhost chlamdb "." "." ".*"

- launch celery workers 

1celery -A chlamdb.celeryapp worker -l info


setup on vital-it

ete3

work with the following variable exported: 


1export QT_QPA_PLATFORM=offscreen
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