- OS: Ubuntu 16.04
- Front-end: Bootstrap
- Back-end: Node.js
- DB: MongoDB
/MULocDeepWeb/MULocDeep is the algorithm module from https://github.com/yuexujiang/MULocDeep
Change two paths to relative path as
/MULocDeepWeb/MULocDeep/utils.py, line 275 & 295:
psiblast_cline = NcbipsiblastCommandline(query=inputfile, db='./MULocDeep/db/swissprot/swissprot',num_iterations=3, evalue=0.001, out_ascii_pssm=pssmfile, num_threads=4)
/MULocDeepWeb/MULocDeep/predict.py, line 147:
model_small.load_weights('./MULocDeep/cpu_models/fold' + str(foldnum) + '_big_lv1_acc-weights.hdf5')
$ apt-get update
$ apt-get install -y
$ apt-get install python3.7
$ apt-get install python3-pip
$ apt-get update && apt-get install -y
$ apt-get install python3-tk
$ python -m pip install numpy scipy
$ python -m pip install biopython
$ python -m pip install h5py
$ python -m pip install tensorflow==1.13.1
$ python -m pip install keras==2.3.0
$ python -m pip install matplotlib
$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz
$ tar zxvpf ncbi-blast-2.9.0+-x64-linux.tar.gz
$ rm ncbi-blast-2.9.0+-x64-linux.tar.gz
$ PATH "$PATH:/ncbi-blast-2.9.0+/bin"
$ curl -sL https://deb.nodesource.com/setup_10.x | sudo -E bash -
$ sudo apt-get install -y nodejs
$ git clone ...
Copy database folder /db directly under MULocDeepWeb/MULocDeep/
/MULocDeepWeb
$ npm install
/MULocDeepWeb
$ sudo service mongod start
$ node app.js
Check file Dockerfile
Check file docker-compose.yml
$ docker-compose up -d
Visit http://localhost:8082/ to check
- assets: including custimize css file, js file and js lib.
- data: store predicting files & result files
- models: including email config model and db schemes models
- MULocDeep: core algorithm
- routes: including different route file
- views: including ejs templates
.
+-- assets
| +-- css
| +-- js
| +-- lib
+-- data
| +-- results
| +-- upload
+-- models
| +-- emailConfig.js
| +-- jobInfo.js
| +-- userInfo.js
+-- MULocDeep
+-- node_modules
+-- routes
| +-- index.js
| +-- jobs.js
| +-- process.js
| +-- results.js
| +-- uploads.js
+-- views
| +-- partials
| +-- footer.js
| +-- header.ejs
| +-- 404.ejs
| +-- CONTACT.ejs
| +-- EXAMPLE.ejs
| +-- JOBINFO.ejs
| +-- JOBSLIST.ejs
| +-- MAP.ejs
| +-- OUTSPACE.ejs
| +-- SEARCH.ejs
| +-- SHOW.ejs
| +-- TOOLS.ejs
| +-- UPLOAD.ejs
+-- app.js
+-- package-lock.json
+-- package.json
+-- docker-compose.yml
+-- Dockerfile
- Modified the display page
- Changed the display of result JSON data
- Modified the example page
- Added features to tables in example pages
- Modified email config
- Added some example locations on the map to test
- Fixed bug: number of total query
- Added CONTACT page
- Added some introduction
- Changed Searching ID Feature to not based on IP
- Added email input feature on job waiting page, update database scheme
- Added estimated time on job waiting page, added time estimating function
- Changed the index to upload page
- Changed the results of predicting to bar chart
- Added check function on vliad FASTA file
- Changed two alerts of uploading to font-end/add two error pages.
- Set Docker.
- Recovered the auto delete model
- Fixed bug: delete folder
- Changed the MAP page UI
- Updated predict script to avoid invalid seq name.
- Updated space function, deleted temp files.
- Updated time estimating function to real
- Added server restart clean function
- Added number of proteins display
- Added space adjust function
- Fixed util.py path config bug
- Updated correct timing function
- Deleted pssm folder
- Changed schedule cleaning to per day
- Updated schedule cleaning time to UTC 6:00:00