Add win32 folder

win32/build_setup.iss

+; Script generated by the Inno Setup Script Wizard.
+; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
+
+[Setup]
+; NOTE: The value of AppId uniquely identifies this application.
+; Do not use the same AppId value in installers for other applications.
+; (To generate a new GUID, click Tools | Generate GUID inside the IDE.)
+AppId={{4B4F7755-28D0-4157-89AA-9752C38E3508}
+AppName=D-Genies
+AppVersion=0.9
+;AppVerName=D-Genies 0.9
+AppPublisher=INRA - Genotoul bioinfo
+AppPublisherURL=http://dgenies.toulouse.inra.fr
+AppSupportURL=http://dgenies.toulouse.inra.fr
+AppUpdatesURL=http://dgenies.toulouse.inra.fr
+DefaultDirName={pf}\Dgenies
+DisableProgramGroupPage=yes
+LicenseFile=data\LICENSE.txt
+OutputBaseFilename=dgenies_setup
+SetupIconFile=data\logo.ico
+Compression=lzma
+SolidCompression=yes
+
+[Languages]
+Name: "english"; MessagesFile: "compiler:Default.isl"
+Name: "french"; MessagesFile: "compiler:Languages\French.isl"
+
+[Tasks]
+Name: "desktopicon"; Description: "{cm:CreateDesktopIcon}"; GroupDescription: "{cm:AdditionalIcons}"; Flags: unchecked
+
+[Files]
+Source: "dist\dgeniesrun\dgeniesrun.exe"; DestDir: "{app}"; Flags: ignoreversion
+Source: "dist\dgeniesrun\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs
+Source: "data\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs
+; NOTE: Don't use "Flags: ignoreversion" on any shared system files
+
+[Icons]
+Name: "{commonprograms}\D-Genies"; Filename: "{app}\dgeniesrun.exe"
+Name: "{commondesktop}\D-Genies"; Filename: "{app}\dgeniesrun.exe"; Tasks: desktopicon
+
+[Run]
+Filename: "{app}\dgeniesrun.exe"; Description: "{cm:LaunchProgram,D-Genies}"; Flags: nowait postinstall skipifsilent
+

win32/data/application.properties

+[global]
+config_dir = ###USER###/dgenies
+upload_folder = ###CONFIG###/tmp
+data_folder = ###CONFIG###/data
+
+threads_local = 4
+
+# Max size of uploaded files (also for files from URL, size uncompressed):
+# Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
+max_upload_size = 3G
+# Max upload file size for all-vs-all (only target):
+# Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
+max_upload_size_ava = 1G
+# Max upload file size (compressed or not, only for uploaded files, not from URL):
+# Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
+max_upload_file_size = 1G
+
+
+[softwares]
+minimap2 = ###SYSEXEC###/../minimap2/minimap2.exe
+
+
+[debug]
+# Debug (enable only for tests)
+enable = False
+log_dir = ###CONFIG###/logs

win32/data/dgenies/INSTALL.md

+Install your own instance
+=========================
+    
+Linux
+-----
+
+### Install
+
+Install in 1 step (as root):
+
+    pip3 install dgenies
+
+Alternatively, you can install it manually:
+
+    git clone https://forgemia.inra.fr/genotoul-bioinfo/dgenies.git
+    cd dgenies
+    pip3 install -r requirements.txt
+    python3 setup.py install
+    
+### Upgrade
+
+#### Standalone mode
+
+    pip3 install dgenies --upgrade
+    
+#### Webserver mode
+
+    dgenies clear -c
+    pip3 install dgenies --upgrade
+    
+Then, you need to restart your webserver.
+    
+    
+    
+Requirements
+------------
+
+D-Genies requires python >= 3.5 to run.
+
+We use minimap2 for mapping. A binary of minimap2 is shipped with the program. Alternatively, you can
+install your own from [their repository](https://github.com/lh3/minimap2).
+
+Some python modules are required (will be automatically installed by the commands above):
+
+    flask==0.12.*
+    Jinja2==2.9.*
+    numpy
+    wget==3.2
+    requests==2.18.*
+    biopython==1.70
+    psutil==5.4.*
+    tendo==0.2.*
+    matplotlib==2.1.*
+    intervaltree==2.1.*
+    argparse==1.4
+    Markdown==2.6.*
+    
+Additional modules for webserver mode:
+
+    Flask-Mail==0.9.*
+    peewee==2.10.2
+    python-crontab==2.2.*
+    
+And if you use a cluster (webserver mode):
+
+    drmaa==0.7.*
+    
+In webserver mode, you must install `mysqlclient` python module (will not be installed automatically) if you use mysql as RDBM.
+    
+    
+How to start
+-------------
+
+You can launch DGenies in `standalone` mode or in `webserver` mode. You can use standalone mode if
+you launch it locally and only one user launch jobs at once. If you are several users to use it
+simultaneously or if you run it on a server, you must run it in webserver mode.
+
+### Standalone mode
+
+Start with the command below:
+
+    dgenies run
+    
+Optional arguments:
+
+`-p <port>` run in a specified port (default: 5000)  
+`--no-browser` don't start the browser automatically
+
+### Webserver mode
+
+*Note: this mode is only available for Unix systems and will NOT work on MS Windows.*
+
+#### Recommended method
+
+Flask webserver (which is used in standalone mode) is not recommended in production servers.  
+So, we recommend using the WSGY module of Apache (or µWSGI + nginx, not documented here).
+
+Once dgenies is installed, you just need to use the `/var/www/dgenies.wsgi` file into your apache
+virtualhost file.
+
+Here is an example of configuration file for apache:
+
+    <VirtualHost *>
+        ServerName <url>
+
+        WSGIDaemonProcess dgenies user=<user> group=<group> threads=8
+        WSGIScriptAlias / /var/www/dgenies/dgenies.wsgi
+        
+        <Directory /var/www/dgenies>
+            WSGIProcessGroup dgenies
+            WSGIApplicationGroup %{GLOBAL}
+            Order deny,allow
+            Allow from all
+        </Directory>
+    </VirtualHost>
+    
+With:  
+`<url>`: the URL of your instance  
+`<user>`: the user who launch the server  
+`<group>`: the group who launch the server
+
+#### Debug method
+
+For debug or for development only, you can launch dgenies through flask in webserver mode:
+
+    dgenies run -m webserver
+    
+Optional parameters:
+
+`-d` run in debug mode  
+`-o <IP>` specify the host into run the application (default: 127.0.0.1, set 0.0.0.0 for distant access)  
+`-p <port>` run in a specified port (default: 5000)  
+`--no-crons` don't run the crons automatically  
+`--no-browser` don't start the browser automatically (always true if *-d* option is given)
+
+
+
+Running with a cluster
+----------------------
+
+If you want to run jobs on a cluster, some configuration is required. We only support SLURM and SGE schedulers. But please note that only SLURM scheduler has been fully tested.
+
+Note: submitting jobs on a cluster is only available for webserver mode.
+
+Jobs are submitted throw the DRMAA library. So you need it for your scheduler. Please see [configuration below](#cluster) to define path to this library.
+
+Also, scripts for preparing data must be moved in a location accessible by all nodes of your cluster. You must move them in a same folder and set the full path to `all_prepare.py` script (full path on the nodes of the cluster) in the configuration file ([see below](#cluster)).
+
+To get these scripts, follow the commands below:
+
+    curl https://forgemia.inra.fr/genotoul-bioinfo/dgenies/raw/master/get_cluster_scripts.py > get_cluster_scripts.py
+    python get_cluster_scripts.py -d <dir>
+    
+With `<dir>`: the folder into save the scripts (must be accessible by cluster nodes).
+
+
+
+Configuration
+-------------
+
+Changing the default configuration is not required for standalone mode, but you can want to custom some parts of the program.
+
+Configuration is stored in the `/etc/dgenies/application.properties` file (linux). The file is divided in 8 parts described below.
+
+To change this file, please copy it into `application.properties.local` (at the same location) to avoid erase of the file on upgrades.
+
+### Global
+
+Main parameters are stored into this section: 
+
+* `config_dir`: where configuration file will be stored.
+* `upload_folder`: where uploaded files will be stored.
+* `data_folder`: where data files will be stored (PAF files and other files used for the dotplot).
+* `threads_local`: number of threads to use for local jobs.
+* `web_url`: public URL of your website.
+* `max_upload_size`: max size allowed for query and target file (-1 to avoid the limit) - size uncompressed.
+* `max_upload_size_ava`: max size allowed for target file for all-vs-all mode (only target given, -1 to avoid the limit) - size uncompressed.
+* `max_upload_file_size`: max size of the uploaded size (real size of the file, compressed or not, -1 to avoid the limit).
+
+For webserver mode only (ignored in standalone mode):
+
+* `batch_system_type`: local for run all jobs locally, sge or slurm to use a cluster scheduler.
+
+### Softwares
+
+Paths to the external software should be set here:
+
+* `minimap2`: path to minimap2 software (keep as it to use built-in)
+
+And if you use a cluster:
+
+* `minimap2_cluster`: path to minimap2 on the cluster
+
+### Debug
+
+Some parameters for debug:
+
+* `enable`: True to enable debug
+* `log_dir`: folder into store debug logs
+
+### Cluster
+
+This section concerns only the webserver mode with *batch_system_type* not set to *local*.
+
+* `drmaa_lib_path`: absolute path to the drmaa library. Required as we use the DRMAA library to submit jobs to the cluster.
+* `native_specs`: how to set memory, time and number of CPU on the cluster (should be kept as default).
+
+By default, small jobs are still launched locally even if *batch_system_type* is not set to *local*, and if not too much of these jobs are running or waiting. This limit can be customized:
+
+* `max_run_local`: max number of jobs running locally (if this number is reached, future jobs will be submitted to the cluster regardless of their size). Set to 0 to run all jobs on the cluster.
+* `max_wait_local`; max number of jobs waiting for a local run (if this number is reached, future jobs will be submitted to the cluster regardless of their size). Set to 0 to run all jobs on the cluster.
+
+You can also customize the size from which jobs are submitted on the cluster. If only one of these limit is reached, the job is submitted on the cluster.
+
+* `min_query_size`: minimum size for the query (uncompressed).
+* `min_size_target`: minimum size for the target (uncompressed).
+
+Other parameters:
+
+* `prepare_script`: absolute path to the all_prepare.py script downloaded in the section [above](#running-with-a-cluster).
+* `python3_exec`: path to python3 executable on the cluster.
+* `memory`: max memory to reserve on the cluster.
+* `memory_ava`: max memory to reserve on the cluster un all-vs-all mode (should be higher than memory).
+* `threads`: number of threads for launching jobs on the cluster (must be a divider of the memory).
+
+### Database
+
+This section concerns only the webserver mode.
+
+In webserver mode, we use a database to store jobs.
+
+* `type`: sqlite or mysql. We recommend mysql for better performances.
+* `url`: path to the sqlite file, or url to the mysql server (localhost if the mysql server is on the same machine).
+
+If type is mysql, some other parameters must be filled:
+
+* `port`: port to connect to mysql (3306 as default).
+* `db`: name of the database.
+* `user`: username to connect to the database.
+* `password`: the associated password.
+
+### Mail
+
+This section concerns only the webserver mode.
+
+At the end of the job, a mail is send to the user to advise him of the end of the job.
+
+* `status`: mail to use for status mail.
+* `reply`: mail to use as reply to.
+* `org`: name of the organisation who send the mail.
+* `send_mail_status`: True to send mail status, False else. Should be True in production.
+
+### Cron
+
+This section concerns only the webserver mode.
+
+We use crons to launch the local scheduler who start jobs, and some script that clean old jobs.
+
+* `clean_time`: time at which we launch the clean job (example: 1h00)
+* `clean_freq`: frequency of the clean job execution
+
+### Jobs
+
+This section concerns only the webserver mode.
+
+Several parameters for jobs:
+
+* `run_local`: max number of concurrent jobs launched locally.
+* `data_prepare`: max number of data prepare jobs launched locally.
+* `max_concurrent_dl`: max number of concurrent upload of files allowed.
+
+
+
+Maintenance
+-----------
+
+The `dgenies` command can be used to do some maintenance staff.
+
+**Clear all jobs:**
+
+    dgenies clear -j [--max-age <age>]
+    
+`--max-age` (opt): set the max age of jobs to delete (default: 0, for all)
+    
+**Clear all log:**
+
+    dgenies clear -l
+    
+**Clear crons (webserver mode):**
+
+    dgenies clear -c
+    
+Gallery
+-------
+
+Note: gallery is only available in webserver mode.
+
+To add a job to the gallery, copy illustrating picture file into the *gallery* folder inside the data folder (*~/.dgenies/data/gallery* as default, create it if not exists). Then use the *dgenies* command:
+
+    dgenies gallery add -i <id_job> -n <name> -q <query_name> -t <target_name> -p <pict_filename>
+    
+With:  
+`id_job`: the name of the job  
+`name`: name of the job to show in the gallery  
+`query_name`: name of the query  
+`target_name`: name of the target  
+`pict_filename`: filename added in the gallery folder (without path)
+
+You can also delete an item from the gallery:
+
+    dgenies gallery del -i <id_job>
+    
+or:
+
+    dgenies gallery del -n <name>
+    
+With `id_job` and `name` as described above. You can add the `--remove-pict` option to remove the picture file from the gallery folder.
+
+Note: first item of the gallery will be shown on home page.
\ No newline at end of file

win32/data/dgenies/doc_run_standalone.md

+How to run a job?
+-----------------
+
+![illustrating](/static/images/D-GENIES-run-standalone.png)
+
+### (1) Main menu
+
+You just need to click on the *run* tab of the main menu, and follow the fields. All results will be stored in the result menu.
+
+### (2) Updatable job name
+
+Required field
+
+An unique job name is set automatically. You could change it. Note that is a job already exists with this name, it will be automatically renamed.
+
+### (3) Target file
+
+Required field
+
+With the selector at the left, you can choose giving a local file or an URL. For a local file, select it by clicking on the button at the right.
+
+File must be in fasta format. We recommend using gzipped files to preserve bandwidth and faster job submission.
+
+Allowed extensions: fa, fasta, fna, fa.gz, fasta.gz, fna.gz
+
+Max file size: ###size### (###size_unc### once uncompressed, ###size_ava### in all-vs-all mode)
+
+### (4) Query file
+
+Optional field
+
+Works like the target file. If not given, target file will be mapped to itself, in all-vs-all mode.
+
+Max file size: ###size### (###size_unc### once uncompressed)
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win32/data/dgenies/static/README.txt

+Copy in this folder all folders and files from the /src/dgenies/static folder

win32/data/dgenies/templates/README.txt

+Copy in this folder all templates files from the /src/dgenies/template folder

win32/dgeniesrun.py

+#!c:\users\ad_miat\appdata\local\programs\python\python36\python.exe
+
+import dgeniesexe
+
+dgeniesexe.run()
\ No newline at end of file