Add Doc fur run a job

src/dgenies/doc_run.md

+How to run a job?
+-----------------
+
+![illustrating](/static/images/D-GENIES-run.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) User email
+
+Required field
+
+Please fill your email. When the mail will be finished, you will receive a mail to inform you that your job is done. Also, some features in the result page will send you a mail to this address.
+
+### (4) 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)
+
+### (5) 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)
\ No newline at end of file

src/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)
\ No newline at end of file

src/dgenies/lib/functions.py

@@ -196,13 +196,14 @@ class Functions:
         Functions.send_fasta_ready(mailer, job_name, sample_name, compressed)
 
     @staticmethod
-    def get_readable_size(size):
-        units = ["Kb", "Mb", "Gb"]
+    def get_readable_size(size, nb_after_coma=1):
+        print(size)
+        units = ["b", "Kb", "Mb", "Gb"]
         i = 0
         while size >= 1024 and i < 3:
             size /= 1024.0
             i += 1
-        return "%.1f %s" % (size, units[i])
+        return str("%." + str(nb_after_coma) + "f %s") % (size, units[i])
 
     @staticmethod
     def get_readable_time(seconds):

src/dgenies/templates/base.html

@@ -66,9 +66,8 @@
                             <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span
                                     class="caret"></span></a>
                             <ul class="dropdown-menu" role="menu">
-                                <li><a href="#">Launch a job</a></li>
-                                <li><a href="#">Zoom</a></li>
-                                <li><a href="#">Filter data</a></li>
+                                <li><a href="/documentation/run">Launch a job</a></li>
+                                <li><a href="#">Results</a></li>
                             </ul>
                         </li>
                         <li class="{% if(menu == 'install') %}active{% endif %}"><a href="/install">Install</a></li>

src/dgenies/views.py

@@ -226,6 +226,34 @@ def get_file(file, gzip=False):  # pragma: no cover
         abort(500)
 
 
+@app.route("/documentation/run", methods=['GET'])
+def documentation_run():
+    with open(os.path.join(app_folder, "doc_run.md" if MODE == "webserver" else "doc_run_standalone.md"), "r",
+              encoding='utf-8') as install_instr:
+        content = install_instr.read()
+    md = Markdown(extensions=[TocExtension(baselevel=1)])
+    max_upload_file_size = config_reader.max_upload_file_size
+    if max_upload_file_size == -1:
+        max_upload_file_size = "no limit"
+    else:
+        max_upload_file_size = Functions.get_readable_size(max_upload_file_size, 0)
+    max_upload_size = config_reader.max_upload_size
+    if max_upload_size == -1:
+        max_upload_size = "no limit"
+    else:
+        max_upload_size = Functions.get_readable_size(max_upload_size, 0)
+    max_upload_size_ava = config_reader.max_upload_size_ava
+    if max_upload_size_ava == -1:
+        max_upload_size_ava = "no limit"
+    else:
+        max_upload_size_ava = Functions.get_readable_size(max_upload_size_ava, 0)
+    content = Markup(md.convert(content)).replace("###size###", max_upload_file_size)\
+                                         .replace("###size_unc###", max_upload_size)\
+                                         .replace("###size_ava###", max_upload_size_ava)
+    toc = Markup(md.toc)
+    return render_template("documentation.html", menu="documentation", title=app_title, content=content, toc=toc, mode=MODE)
+
+
 @app.route("/install", methods=['GET'])
 def install():
     with open(os.path.join(app_folder, "INSTALL.md"), "r", encoding='utf-8') as install_instr:
@@ -233,7 +261,7 @@ def install():
     md = Markdown(extensions=[TocExtension(baselevel=1)])
     content = Markup(md.convert(content))
     toc = Markup(md.toc)
-    return render_template("install.html", menu="install", title=app_title, content=content, toc=toc, mode=MODE)
+    return render_template("documentation.html", menu="install", title=app_title, content=content, toc=toc, mode=MODE)
 
 
 @app.route("/paf/<id_res>", methods=['GET'])