[med-svn] [mobyle-tutorials] 07/12: New upstream version 1.5.0
Andreas Tille
tille at debian.org
Tue Nov 28 15:32:32 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mobyle-tutorials.
commit 5ba785aa6c2a5eefca15b93eccfbd75b6d3051b4
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 28 16:29:41 2017 +0100
New upstream version 1.5.0
---
Alignment_formats.xml | 239 ++++++++++++++++++++++++++++++++++++++++
Sequences_formats.xml | 235 +++++++++++++++++++++++++++++++++++++++
debian/README.Debian | 2 -
debian/changelog | 15 ---
debian/compat | 1 -
debian/control | 24 ----
debian/copyright | 36 ------
debian/get-orig-source | 12 --
debian/links | 1 -
debian/mobyle-tutorials.install | 1 -
debian/rules | 11 --
debian/source/format | 1 -
debian/watch | 3 -
phylip_phyml_format.xml | 54 +++++++++
registration.xml | 44 ++++++++
setpbystep.xml | 104 +++++++++++++++++
16 files changed, 676 insertions(+), 107 deletions(-)
diff --git a/Alignment_formats.xml b/Alignment_formats.xml
new file mode 100644
index 0000000..109e111
--- /dev/null
+++ b/Alignment_formats.xml
@@ -0,0 +1,239 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- XML Authors: Bertrand Néron -->
+<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
+<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
+<tutorial>
+ <head>
+ <name>Alignment_format</name>
+ <version>1.0</version>
+ <doc>
+ <title>Alignment formats</title>
+ <description>
+ <text lang="en">common used formats for aligned sequences</text>
+ </description>
+ <authors>N. Joly</authors>
+ </doc>
+ <category>data formats</category>
+ <interface type="tutorial">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+ <p>This document illustrates some common formats used for aligned sequences
+ representation.
+ </p>
+ <dl>
+ <dt>
+ <strong>
+ <a name="clustal" class="item">
+ <strong>CLUSTAL</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>CLUSTAL W (1.82) multiple sequence alignment</pre>
+<pre>
+MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTL
+MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTL
+MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTL
+MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------
+ *:** *:**:**:*:.::**:***:*::***</pre>
+<pre>
+MALK_ECOLI LRMIAGLETITSGDLACRRLHKEPGV
+MALK_SALTY LRMIAGLETITSGDLACRRLHQEPGV
+MALK_ENTAE LRMIAGLETVTSGDL-----------
+MALK_PHOLU LRM-----------------------
+ ***</pre>
+ <p>
+ <strong>Warning</strong>
+ : Names must not contain spaces or exceed 30 characters.
+ </p>
+ </dd>
+ <dt>
+ <strong>
+ <a name="fasta" class="item">
+ <strong>FASTA</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+<pre>
+>MALK_ECOLI
+MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
+GLETITSGDLACRRLHKEPGV
+>MALK_SALTY
+MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
+GLETITSGDLACRRLHQEPGV
+>MALK_ENTAE
+MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
+GLETVTSGDL-----------
+>MALK_PHOLU
+MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------LRM--
+---------------------</pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="mega" class="item">
+ <strong>MEGA</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+<pre>
+#mega
+!Title Multiple Sequence Alignment;
+</pre>
+<pre>
+#MALK_ECOLI
+MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
+GLETITSGDLACRRLHKEPGV
+#MALK_SALTY
+MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
+GLETITSGDLACRRLHQEPGV
+#MALK_ENTAE
+MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
+GLETVTSGDL-----------
+#MALK_PHOLU
+MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
+---------------------</pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="msf" class="item">
+ <strong>MSF</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+<pre>
+!!AA_MULTIPLE_ALIGNMENT 1.0
+PileUp of: @pep.list
+</pre>
+<pre>
+ msf.seq MSF: 55 Type: P Nov 22, 2001 11:02 Check: 2529 ..
+</pre>
+<pre>
+ Name: m73237 Len: 655 Check: 7493 Weight: 1.00
+ Name: l28824 Len: 655 Check: 5456 Weight: 1.00
+ Name: u04379 Len: 655 Check: 9580 Weight: 1.00
+</pre>
+<pre>//</pre>
+<pre>
+ 1 50
+m73237 ~~~~~MADSA NHLPFFFGQI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
+l28824 MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
+u04379 ~~~~~MPDPA AHLPFFYGSI SRAEAEEHLK LAGMADGLFL LRQCLRSLGG
+</pre>
+<pre>
+ 51
+m73237 ~~~~~
+l28824 ~~~~~
+u04379 AACG*
+</pre>
+ <p>
+ <strong>Warning</strong>
+ : This format cannot handle more than 500 sequences in a
+ single alignment.
+ </p>
+ </dd>
+ <dt>
+ <strong>
+ <a name="nexus" class="item">
+ <strong>NEXUS</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+<pre>
+#NEXUS</pre>
+<pre>
+begin data;
+ dimensions ntax=2 nchar=89;
+ format datatype=Protein interleave gap=- missing='.';
+ matrix
+[ 1 50]
+btdDm -------AQQQQHHLHMQQAQHH-----------LHLSH------QQAQQ
+TSp1 --------------------AEH-----------PSLR--------GTPL</pre>
+<pre>
+[ 51 80]
+btdDm YACPICSKKFSRSDHLSKHKKTHF------
+TSp1 FACPICNKRFMRSDHLAKHVKTHN------</pre>
+<pre>
+ ;
+endblock;</pre>
+ <p>
+ <strong>Warning</strong>
+ : Text enclosed in brackets is considered as comment, and
+ thus ignored.
+ </p>
+ </dd>
+ <dt>
+ <strong>
+ <a name="phylip" class="item">
+ <strong>PHYLIP</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <p>Sequential (PHYLIPS):</p>
+<pre>
+ 2 109
+ATISA1 GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDG
+ ENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDE
+ YGHTKGGN---
+POTISA1 GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKDG
+ ENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMGDE
+ YGHTKGGN---
+</pre>
+<p>Interleaved (PHYLIPI):</p>
+<pre>
+ 2 109
+ATISA1 GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND
+POTISA1 GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD</pre>
+<pre>
+ GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG
+ GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG</pre>
+<pre>
+ DEYGHTKGGN---
+ DEYGHTKGGN---
+</pre>
+ <p>
+ <strong>Warning</strong>
+ : Species names may not contain characters `( ) : ; , [ ]'
+ and exceed 10 characters.
+ </p>
+ </dd>
+ <dt>
+ <strong>
+ <a name="stockholm" class="item">
+ <strong>STOCKHOLM</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+<pre>
+# STOCKHOLM 1.0
+</pre>
+<pre>
+MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
+MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
+MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
+MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
+</pre>
+<pre>
+MALK_ECOLI RCHLFREDGTACRRLHKEPGV
+MALK_SALTY RCHLFREDGSACRRLHQEPGV
+MALK_ENTAE ---------------------
+MALK_PHOLU ---------------------
+//
+</pre>
+ </dd>
+ </dl>
+ </div>
+ </interface>
+ </head>
+</tutorial>
diff --git a/Sequences_formats.xml b/Sequences_formats.xml
new file mode 100644
index 0000000..f30680b
--- /dev/null
+++ b/Sequences_formats.xml
@@ -0,0 +1,235 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- XML Authors: Bertrand Néron -->
+<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
+<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
+<tutorial>
+ <head>
+ <name>Sequences_formats</name>
+ <version>1.0</version>
+ <doc>
+ <title>Sequences formats</title>
+ <description>
+ <text lang="en">common used formats for sequences</text>
+ </description>
+ <authors>N. Joly</authors>
+ </doc>
+ <category>data formats</category>
+ <interface type="tutorial">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+ <p>This document illustrates some common formats used for sequences representation.</p>
+ <dl>
+ <dt>
+ <strong>
+ <a name="embl" class="item">
+ <strong>EMBL</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+ ID MMVASPHOS standard; RNA; EST; 140 BP.
+ AC X97897;
+ DE M.musculus mRNA for protein homologous to
+ DE vasodilator-stimulated phosphoprotein
+ SQ Sequence 140 BP; 25 A; 58 C; 39 G; 17 T; 1 other;
+ ttctcccaga agctgactct atggngaccc cgagagagac tgagcagaac 60
+ ccccgcaccc ctgcacttcc aatcaggggc gccccgggag cactccccgt 120
+ ccgccctccg cgcagccatg 140
+ //
+ </pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="fasta" class="item">
+ <strong>FASTA</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+ >MMVASPHOS
+ ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
+ ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
+ ccgccctccgcgcagccatg
+ </pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="gcg" class="item">
+ <strong>GCG</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+!!NA_SEQUENCE 1.0
+ (No documentation)
+ dna1.txt Length: 88 Nov 22, 2001 14:38 Type: N Check: 3818 ..
+
+ 1 TAGTCGTAGT CGGAGCGATG CTGACGATGA CGATGACGAT CGTAGCTGAT
+
+ 51 CGATCGAGCT GATGCTGATC GAGCTAGCTG ATCGATCG
+
+ </pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="gde" class="item">
+ <strong>GDE</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+ #sample1
+ TTCAAGAGAAACAGCGGCCAAGGAAAAGACTCGGCATGATTGTCCATAGCTTACAAAGCG
+ #sample2
+ TTCAAGAGAAACAGCGGCTGGGGGAAAGACTCGTCCTGATTGCCTGTAGATGGTAAAGCG
+
+ </pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="genbank" class="item">
+ <strong>GENBANK</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+LOCUS HUMHBV1 130 bp DNA PRI 17-JUN-1993
+DEFINITION Human DNA/endogenous Hepatitis B virus (HBV) DNA, left
+ host viral junction.
+ACCESSION M15770
+BASE COUNT 32 a 43 c 29 g 26 t
+ORIGIN
+ 1 agcgggcagt gcagctgctt ggacagcagg ggtgtttctt caacccaggc
+ 61 ctcctgtcac aacaggccca ttcaattctg aacctgcaag ccaactccaa
+ 121 cctcttttcc cagggggaac caaaaaccct
+//
+
+ </pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="ig" class="item">
+ <strong>IG</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+; comment
+U03518
+AACCTGCGGAAGGATCATTACCGAGTGCGGGTCCTTTGGGCCCAACCTCCCATCCGTGTC
+TATTGTACCCTGTTGCTTCGGCGGGCCCGCCGCTTGTCGGCCGCCGGGGGGGCGCCTCTG
+TGAGTTGATTGAATGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGC1
+ </pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="nbrf" class="item">
+ <strong>NBRF</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+>P1;CCHU
+cytochrome c [validated] - human
+MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
+GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
+ </pre>
+ </dd>
+
+ <dt>
+ <strong>
+ <a name="nbrf" class="item">
+ <strong>NBRF (pir)</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+>P1;CCHU
+cytochrome c [validated] - human
+MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
+GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
+ </pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="codata" class="item">
+ <strong>CODATA</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+ENTRY CCHU #type complete
+TITLE cytochrome c [validated] - human
+ACCESSIONS A31764; A05676; I55192; A00001
+SUMMARY #length 105 #molecular-weight 11749 #checksum 3247
+SEQUENCE
+ 5 10 15 20 25 30
+ 1 M G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G
+ 31 P N L H G L F G R K T G Q A P G Y S Y T A A N K N K G I I W
+ 61 G E D T L M E Y L E N P K K Y I P G T K M I F V G I K K K E
+ 91 E R A D L I A Y L K K A T N E
+///
+ </pre>
+ </dd>
+ <dt>
+ <strong>
+ <a name="raw" class="item">
+ <strong>RAW</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
+ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
+ccgccctccgcgcagccatg
+ </pre>
+ <p>
+ <strong>Warning</strong>
+ : This format cannot handle more than one sequence per file.
+ </p>
+ </dd>
+ <dt>
+ <strong>
+ <a name="swissprot" class="item">
+ <strong>SWISSPROT</strong>
+ </a>
+ </strong>
+ </dt>
+
+ <dd>
+ <pre>
+ID 100K_RAT STANDARD; PRT; 149 AA.
+AC Q62671;
+DE 100 kDa protein (EC 6.3.2.-).
+SQ SEQUENCE 149 AA; 17004 MW; D06484B8BC29112E CRC64;
+ MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK
+ PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN
+ SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV
+//
+ </pre>
+ </dd>
+ </dl>
+
+ </div>
+ </interface>
+ </head>
+</tutorial>
diff --git a/debian/README.Debian b/debian/README.Debian
deleted file mode 100644
index 81e91f8..0000000
--- a/debian/README.Debian
+++ /dev/null
@@ -1,2 +0,0 @@
-By default, tutorials are not deployed.
-User should deploy one or all tutorials to make it visible on the portal.
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 7886c77..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,15 +0,0 @@
-mobyle-tutorials (1.5.0-2) unstable; urgency=medium
-
- * Update homepage
- * cme fix dpkg-control
- * debhelper 9
- * Enhance long description
-
- -- Andreas Tille <tille at debian.org> Tue, 12 Jan 2016 09:50:35 +0100
-
-mobyle-tutorials (1.5.0-1) unstable; urgency=low
-
- * First release (Closes: #700859)
-
- -- Olivier Sallou <osallou at debian.org> Mon, 18 Feb 2013 12:28:22 +0100
-
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index f6d0338..0000000
--- a/debian/control
+++ /dev/null
@@ -1,24 +0,0 @@
-Source: mobyle-tutorials
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>,
- Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mobyle/mobyle-tutorials/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mobyle/mobyle-tutorials/trunk/
-Homepage: https://projets.pasteur.fr/projects/mobyle/wiki/Download
-
-Package: mobyle-tutorials
-Architecture: all
-Depends: ${misc:Depends},
- mobyle (>= 1.5+dfsg)
-Description: program tutorials for the mobyle portal
- Mobyle is a framework and web portal specifically aimed at the integration of
- bioinformatics software and databanks. It generates a web interface from an xml
- description for command-line based tools.
- It can submit jobs locally or using DRM systems.
- .
- This package contains a set of tutorials for the mobyle framework.
- Those tutorials can be deployed to be used on the portal.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 17a8485..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,36 +0,0 @@
-Format: http://anonscm.debian.org/viewvc/dep/web/deps/dep5.mdwn?revision=174
-Upstream-Name: mobyle
-Source: ftp://ftp.pasteur.fr/pub/gensoft/projects/mobyle/Tutorials-*.tgz
-
-Files: *
-Copyright: 2011 Herve Menager <hmenager at pasteur.fr>
- 2011 Bertrand Néron <bneron at pasteur.fr>
- 2011 Nicolas Joly <njoly at pasteur.fr>
- 2011 Corinne Maufrais <maufrais at pasteur.fr>
- 2011 Sandrine Larroudé <slarroud at pasteur.fr>
- 2011 Pierre Tufféry <pierre.tuffery at univ-paris-diderot.fr>
- 2011 Catherine Letondal <letondal at pasteur.fr>
-License: LGPL-2+
-
-Files: debian/*
-Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
-License: LGPL-2+
-
-License: LGPL-2+
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Library General Public
- License as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later version.
- .
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Library General Public License for more details.
- .
- You should have received a copy of the GNU Library General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
- .
- On Debian systems, the complete text of the GNU Library General
- Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2".
-
diff --git a/debian/get-orig-source b/debian/get-orig-source
deleted file mode 100755
index 0a7ffbb..0000000
--- a/debian/get-orig-source
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash
-
-set -e
-
-PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSION=`uscan --verbose --force-download |
- grep "Newest version on remote site is .* local version is .*" |
- head -n 1 |
- sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
-
-mkdir -p ../tarballs
-
diff --git a/debian/links b/debian/links
deleted file mode 100644
index 8cf047f..0000000
--- a/debian/links
+++ /dev/null
@@ -1 +0,0 @@
-var/lib/mobyle/tutorials usr/share/mobyle/core/Services/Tutorials
diff --git a/debian/mobyle-tutorials.install b/debian/mobyle-tutorials.install
deleted file mode 100644
index 29a1230..0000000
--- a/debian/mobyle-tutorials.install
+++ /dev/null
@@ -1 +0,0 @@
-*.xml var/lib/mobyle/tutorials/
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index e529249..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/make -f
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-%:
- dh $@
-
-
-get-orig-source:
- bash debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index a4aff4e..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=3
-
-opts=passive,filenamemangle=s/Tutorials/mobyle-tutorials/ ftp://ftp.pasteur.fr/pub/gensoft/projects/mobyle/Tutorials-(\d+\.\d+\.\d+)\.tar\.gz debian uupdate
diff --git a/phylip_phyml_format.xml b/phylip_phyml_format.xml
new file mode 100644
index 0000000..3c5852b
--- /dev/null
+++ b/phylip_phyml_format.xml
@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- XML Authors: Bertrand Néron -->
+<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
+<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
+<tutorial>
+ <head>
+ <name>phylip_phyml_format</name>
+ <doc>
+ <title>Phylip/Phyml formats incompatibilities</title>
+ <description>
+ <text lang="en">problem with phylip and phyml alignment formats</text>
+ </description>
+ <authors>B. Néron</authors>
+ </doc>
+ <interface type="tutorial">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+ <h3>Phylip format is defined as following:</h3>
+<p><span style="font-style:italic">"The name should be ten characters in length, filled out to the full ten characters by blanks if shorter.
+Any printable ASCII/ISO character is allowed in the name, except for parentheses ("(" and ")"),
+square brackets ("[" and "]"), colon (":"), semicolon (";") and comma (",").
+If you forget to extend the names to ten characters in length by blanks, the program will get out of
+synchronization with the contents of the data file, and an error message will result."</span>
+(for complete description of phylip format see:
+<a href="http://bioweb2.pasteur.fr/docs/phylip/doc/main.html" target="_blank">http://bioweb2.pasteur.fr/docs/phylip/doc/main.html</a>)</p>
+
+<h3>Phyml declare using Phylip format but instead it uses a variant format:</h3>
+<p style="font-style:italic">"One slight difference with PHYLIP format deals with sequence name lengths.
+While PHYLIP format limits this length to ten characters,
+PhyML can read up to hundred character long sequence names.
+Blanks and the symbols “(),:” are not allowed within sequence names"</p>
+
+<p>These two formats are in some case non compliant.
+The program we use to detect sequences format and convert them is not able to use Phyml format, so it convert sequence in Phylip.
+When sequences name are longer than 10 characters the resulting file is not compliant to use with Phyml
+(the sequence names are truncated to 10 characters and there is no space between name and sequence).
+It exists a workaround to this problem.</p>
+
+<ol>
+ <li>from an alignment in fasta format, use <a href="#forms::fastaRename" class="link">fastaRename</a>, to produce 2 files:
+ <ul>
+ <li style="margin-left: 1em;">one with your sequences where the name was replaced by a short id</li>
+ <li style="margin-left: 1em;">one with the mapping between real names and the ids</li>
+ </ul>
+ </li>
+ <li>use the file with short ids in your analyses as Phyml, MorePhyml,...</li>
+ <li>finally to have a tree with the original names use <a href="#forms::nw_rename" class="link">nw_rename</a> and use the
+ tree generated at the previous step and the file of mapping from the first step.
+ It will produce a tree with the right names.</li>
+</ol>
+
+ </div>
+ </interface>
+ </head>
+</tutorial>
\ No newline at end of file
diff --git a/registration.xml b/registration.xml
new file mode 100644
index 0000000..843585a
--- /dev/null
+++ b/registration.xml
@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- XML Authors: Bertrand Néron -->
+<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
+<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
+<tutorial>
+ <head>
+ <name>registration</name>
+ <version>1.0</version>
+ <doc>
+ <title>benefits to register</title>
+ <description>
+ <text lang="en">benefits to register</text>
+ </description>
+ <authors>H. Ménager</authors>
+ </doc>
+ <interface type="tutorial">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+ <h2>What are the benefits of a registered account?</h2>
+
+ <p>
+ You can use the portal without registering at all. This means that you are welcome as a guest. The results of your jobs will be available for a
+ limited time, even if you exit the portal for a short while.
+ However, you will not be able to use them if you connect from another place.
+ </p>
+
+ <p>
+ Registration enables you to store your bookmarked data and results on the server, without any time limit (as long as we can provide enough disk space of
+ course!).
+ You can also connect using the same e-mail and password from any place.
+ </p>
+
+ <h2>How to register?</h2>
+
+ <p>
+ Click on the <i>sign-in</i> link located on the top right of the page, then click on <i>register</i>.
+ Enter your e-mail, and pick a password (this password is specific to
+ the portal). Once submitted, you will receive an e-mail requesting your confirmation for this registration.
+ You can then save your data, and access them from anywhere.
+ </p>
+
+ </div>
+ </interface>
+ </head>
+</tutorial>
\ No newline at end of file
diff --git a/setpbystep.xml b/setpbystep.xml
new file mode 100644
index 0000000..ef5abb0
--- /dev/null
+++ b/setpbystep.xml
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- XML Authors: Bertrand Néron -->
+<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
+<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
+<tutorial>
+ <head>
+ <name>stepbystep</name>
+ <version>1.0</version>
+ <doc>
+ <title>Step by step tutorial</title>
+ <description>
+ <text lang="en">how to use Mobyle step by step</text>
+ </description>
+ <authors>H. Ménager</authors>
+ </doc>
+ <interface type="tutorial">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+
+ <h2>Step by step tutorial</h2>
+
+ <p>
+ Welcome to Mobyle, a portal to run bioinformatics analyses. This tutorial is interactive: it helps you to open forms, navigate through the
+ portal and fill some fields. At any time, you can come back here by clicking on the
+ <a href="#" onclick="$('tutorials').showTab();">Tutorials</a>
+ tab above.
+ </p>
+
+ <h3>Running an analysis</h3>
+
+ <p>
+ Let's start by running a first analysis: predict a protein membrane topology with the <b>toppred</b> program.
+ Clicking<a href="#forms::toppred" class="link">here</a>
+ opens the <b>toppred</b> form.
+
+ The first field is for the protein sequence. You can paste the following data:
+ </p>
+ <pre>>sp|P02914|MALK_ECOLI MALTOSE/MALTODEXTRIN TRANSPORT ATP-BINDING PROTEIN MALK.
+ MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL
+ FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKPAGAKKEVINQRVNQVAEV
+ LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH
+ KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN
+ FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVIL
+ EGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGT
+ ACRRLHKEPGV
+ </pre>
+ Then launch the program by clicking on the Run button.
+ <p>
+ When finished, the results are available under the <a href="#jobs" class="link">Jobs</a>
+ tab. The output starts by some details on the job, followed by the output files. You can return to the form anytime by clicking on
+ <a href="#forms::toppred" class="link">its tab</a>, at the top of the page.
+ </p>
+
+ <h3>Using the databox</h3>
+
+ <p>
+ You can input data either by copy/paste, file loading, database fetch, or selection of the output from a previous analysis. Let us try this with
+ some examples.
+ </p>
+
+ <h4>- file loading</h4>
+ If you don't have any sequence file, you can save the following sequences into a file on your disk.
+ <br/>
+ <textarea rows="11">>MALK_ECOLI
+ MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
+ GLETITSGDLACRRLHKEPGV
+ >MALK_SALTY
+ MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
+ GLETITSGDLACRRLHQEPGV
+ >MALK_ENTAE
+ MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
+ GLETVTSGDL
+ >MALK_PHOLU
+ MSSVTLRNVSKAYGETIISKNINLEIQEGEFLRM
+ </textarea>
+ Then open the <a href="#forms::clustalw-multialign" class="link">clustalw-multialign</a>
+ form and load your sequences file. Then run the program.
+ <h4>- database</h4>
+ Go back to our <a href="#forms::toppred" class="link">toppred</a>
+ form, hit the "DB" checkbox and enter: MALK_ECOLI into the input field. This fetchs you the corresponding Swissprot entry.
+ <h4>- previous analysis</h4>
+ Open the
+ <a href="#forms::protpars" class="link">protpars</a>
+ form and hit the "Result" checkbox. A menu is available providing access to the sequences previously aligned by Clustalw. Note that you could
+ also have directly input your alignment from the
+ <a href="#jobs" class="link">clustalw result</a>
+ : go to the alignment, select "protpars-infile" from the "pipe it to" menu below the box, and hit "go".
+
+ <h3>Retrieving results later</h3>
+ <p>
+ Results will be available as long as the server keeps the corresponding files. To access to the results of a previously run job, use the "Jobs" drawer on
+ the left.
+ </p>
+ <h3>Searching for programs</h3>
+ <p>
+ The left panel displays 4 "drawers", in order to help you navigate in the portal. The first one provides a list of the available programs,
+ classified by bioinformatics domain. By default, all programs are listed, but you can filter this long list by providing a search term in the
+ <b>search for</b>
+ field. For instance, enter the term "matrix" - notice that you don't need to hit return to start the search. Only the program having the word
+ "matrix" in their description will be displayed. When mousing over the name of the program, the information bullet displays the matched text.
+ </p>
+ </div>
+ </interface>
+ </head>
+</tutorial>
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