first public commit

.gitignore

+*.pyc
+*.db
+*.sql
+*.log
+pypy
+tosql
+win/
+data/
+introgression_viewer.tgz
+introgression_viewer.xz
+static/FileSaver.js/demo/
+static/FileSaver.js/git/
+84_walk
+*.schema
+*.old
+out.png
+vcfmerger/aux/pypy-2.0/
+vcfmerger/pypy-2.0/
+.git2
+lin/
+.nfs*
+.idea/
+nohup.out
+*.tar.gz
+checkout

LICENSE

+The MIT License (MIT)
+
+Copyright (c) <year> <copyright holders>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

README.md

+Introgression Viewer
+Saulo Aflitos - 2013-2014
+sauloalves.aflitos@wur.nl
+Cluster Bioinformatics
+Plant Research International - PRI
+Wageningen University and Research Centre - WageningenUR
+
+1. Introduction
+2. Methodology
+3. Installation
+3.1. Clone Introgression browser
+3.1.1. Processing
+3.1.2. Server
+3.2. Install dependencies
+3.2.2. Server
+3.2.3. Server add-ons
+3.2.4. System
+4. Run
+4.1. Processing
+4.2. Server
+5. Run
+5.1. Processing
+5.2. Server
+6. Acknowledgements
+
+
+
+1. Introduction
+
+2. Methodology
+This set of scripts takes as input a series of Variant Call Files (VCF) of species mapped against a single reference.
+
+After a series of conversions, all homozigous Single Nucleotide Polymorphisms (SNP) are extracted while ignoring heterozigous SNPS (hetSNP), Multiple Nucleotide Polymorphisms (MNP) and Insertion/Deletion events (InDel).
+
+For each individual, the reference's nucleotide will be assigned unless a SNP is presented. If any individual has a MNP, hetSNP or InDel at a given position, this position is skipped entirely.
+
+A General Feature Format (GFF) describing coordinates is used to split the genome into segments. Those segments can be genes, even sized fragments (10kb, 50kb, etc) or particular segments of interest as long as the coordinates are the same as the VCF files. A auxiliary script is provided to generate evenly sized segments.
+
+For each selected segment a fasta file will be generated and FastTree will create a distance matrix and a Newick Tree. After all data has been processed, the three files (fasta, matrix and newick) will be read and converted to a database.
+
+The webserver scripts will read and serve the data to a web browser. There are three scripts, a main script serves the data and two auxiliary servers to perform on-the-fly clustering and image conversion (from SVG to PNG).
+
+
+
+
+3. Installation
+3.1. Clone Introgression browser
+    Clone or download Introgression Browser.
+
+
+3.1.1. Processing
+    Add your files under data subfolder.
+    Add vcfmerger subfolder to your path or create symbolic links inside the data folder.
+
+
+3.1.2. Server
+    Get a database and modify config.py accordingly.
+    The databases are are multiplatform.
+
+
+3.2. Install dependencies
+3.2.1. Processing
+    Check if FastTree runs in your machine (Linux only)
+    Install python dependencies:
+        sqlalchemy
+    Install pypy (Optional but speeds up analysis)
+
+
+3.2.2. Server
+    Install python
+    Install python dependencies:
+        sqlalchemy - already in virtualenv
+        flask - already in virtualenv
+	#py-editdist - already in vcfmerger/aux/ - wget 'https://py-editdist.googlecode.com/files/py-editdist-0.3.tar.gz'
+	#fastcluster
+	pymix
+
+3.2.3. Server add-ons
+    Install python dependencies:
+        on-the-fly clustering:
+            numpy
+            scipy
+        PNG download:
+            wand
+
+3.2.4. System
+	apt-get update
+	apt-get install build-essential checkinstall
+	apt-get install python-setuptools python-dev
+	apt-get install python-numpy python-scipy python-matplotlib python-pandas python-sympy
+	apt-get install libmagickwand-dev
+	apt-get install sqlite3 libsqlite3-dev
+
+	easy_install pip
+	easy_install flask
+	easy_install sqlalchemy
+	easy_install wand
+
+3.2.5. Vistualization
+3.2.5.1. VirtualBox
+	share your data folder as "data" shared folder
+	wget http://download.virtualbox.org/virtualbox/4.3.6/VBoxGuestAdditions_4.3.6.iso
+	mkdir vbox
+	mount VBoxGuestAdditions_4.3.6.iso vbox
+	cd vbox
+	./VBoxLinuxAdditions.run
+	cd ..
+	umount vbox
+	edit /etc/fstab adding
+		data /media/data vboxsf re 0 0
+	mount -a
+	ls /media/data
+
+3.2.5.1. VMware
+	share your data folder as "data" shared folder
+	attach the VMware tools
+	mkdir /mnt/cdrom
+	mount /dev/cdrom /mnt/cdrom
+	mkdir ~/vm
+	cd ~/vm
+	tar xvf /dev/cdrom/VMwareTools-9.6.1-1378637.tar.gz
+	cd vmware-tools-distrib
+	./vmware-install.pl -d
+	cd ../..
+	rm -rf vm
+	ls /mnt/hgfs/data
+	
+
+4. Configuration
+4.1. Processing
+    Inside the "data" folder create a tab delimited file containing path to the VCF files and the "pretty" name for them. The first column is ignored.
+        1	input/RF_001_SZAXPI008746-45.vcf.gz	Moneymaker (001)
+        0	input/RF_002_SZAXPI009284-57.vcf.gz	Alisa Craig (002)
+        0	input/RF_003_SZAXPI009285-62.vcf.gz	Gardeners Delight (003)
+
+
+4.2. Server
+    Edit config.py to create users, configure the server's port, the encryption key, describe available databases and decide whether to use SQL ot RAM database.
+
+
+
+
+5. Run
+5.1. Processing
+    Merge VCF files:
+        vcfmerger/vcfmerger.py short.lst
+            OUTPUT: short.lst.vcf.gz
+                #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  FILENAMES
+                SL2.40ch00      280     .       A       C       .       PASS    NV=1;NW=1;NS=1;NT=1;NU=1        FI      S cheesemaniae (055)
+                SL2.40ch00      284     .       A       G       .       PASS    NV=1;NW=1;NS=1;NT=1;NU=1        FI      S cheesemaniae (054)
+                SL2.40ch00      316     .       C       T       .       PASS    NV=1;NW=1;NS=1;NT=1;NU=1        FI      S arcanum (059)
+                SL2.40ch00      323     .       C       T       .       PASS    NV=1;NW=1;NS=1;NT=1;NU=1        FI      S arcanum (059)
+                SL2.40ch00      332     .       A       T       .       PASS    NV=1;NW=1;NS=1;NT=1;NU=1        FI      S pimpinellifolium (047)
+                SL2.40ch00      362     .       G       T       .       PASS    NV=1;NW=1;NS=1;NT=1;NU=1        FI      S galapagense (104)
+                SL2.40ch00      385     .       A       C       .       PASS    NV=1;NW=1;NS=1;NT=1;NU=1        FI      S neorickii (056)
+                SL2.40ch00      391     .       C       T       .       PASS    NV=1;NW=1;NS=6;NT=6;NU=6        FI      S chiemliewskii (052),S neorickii (056),S arcanum (059),S habrochaites glabratum (066),S habrochaites glabratum (067),S habrochaites (072)
+
+
+    Simplify merged VCF deleting hetSNP, MNP and InDels:
+        vcfmerger/vcfsimplify.py short.lst.vcf.gz
+            OUTPUT: short.lst.vcf.gz.filtered.vcf.gz
+                SL2.40ch00      391     .       C       T       .       PASS    NV=1;NW=1;NS=6;NT=6;NU=6        FI      S arcanum (059),S chiemliewskii (052),S habrochaites (072),S habrochaites glabratum (066),S habrochaites glabratum (067),S neorickii (056)
+                SL2.40ch00      416     .       T       A       .       PASS    NV=1;NW=1;NS=6;NT=6;NU=6        FI      S arcanum (059),S chiemliewskii (052),S habrochaites (072),S habrochaites glabratum (066),S habrochaites glabratum (067),S neorickii (056)
+                SL2.40ch00      424     .       C       T       .       PASS    NV=1;NW=1;NS=5;NT=5;NU=5        FI      LA0113 (039),S cheesemaniae (054),S pimpinellifolium (044),S pimpinellifolium unc (045),S pimpinellifolium (047)
+
+
+    Generate even sized fragments (if needed):
+        vcfmerger/aux/fasta_spacer.py GENOME.fa 50000
+            OUTPUT: GENOME.fa.50000.gff
+                SL2.40ch00      .       fragment_10000  1       10000   .       .       .       Alias=Frag_SL2.40ch00g10000_1;ID=fragment:Frag_SL2.40ch00g10000_1;Name=Frag_SL2.40ch00g10000_1;length=10000;csize=21805821
+                SL2.40ch00      .       fragment_10000  10001   20000   .       .       .       Alias=Frag_SL2.40ch00g10000_2;ID=fragment:Frag_SL2.40ch00g10000_2;Name=Frag_SL2.40ch00g10000_2;length=10000;csize=21805821
+
+
+    Filter with gff:
+        vcfmerger/vcffiltergff.py -k -f PROJNAME -g GENOME.fa_50000.gff -i short2.lst.vcf.gz.simplified.vcf.gz 2>&1 | tee short2.lst.vcf.gz.simplified.vcf.gz.log
+            OUTPUT:
+                #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  FILENAMES
+                SL2.40ch00      391     .       C       T       .       PASS    NV=1;NW=1;NS=6;NT=6;NU=6        FI      S arcanum (059),S chiemliewskii (052),S habrochaites (072),S habrochaites glabratum (066),S habrochaites glabratum (067),S neorickii (056)
+
+
+    Concatenate the SNPs of each fragment into FASTA:
+        find PROJNAME -name '*.vcf.gz' | xargs -I{} -P50 bash -c 'vcfmerger/vcfconcat.py -f -i {} 2>&1 | tee {}.concat.log'
+            OUTPUT: PROJNAME/CHROMOSOME/short2.lst.vcf.gz.simplified.vcf.gz.filtered.vcf.gz.SL2.40ch01.000090300001-000090310000.Frag_SL2.40ch01g10000_9031.vcf.gz.SL2.40ch01.fasta
+                >Moneymaker_001
+                ATAATCTAGCTGGAACCCTTGTTTTTCTCGCGATTGGGGTTCAAGTGCACACCACATGTC
+                AGGGA
+                >Alisa_Craig_002
+                ATAATCTAGCTGGAACCCTTGTTTTTCTTGCGATTGGGGTTCAAGTGCGCGCTGCGTGAC
+                AGGAA
+
+
+    Run FastTree in each of the FASTA files:
+        export OMP_NUM_THREADS=3
+        find PROJNAME -name '*.fasta' | sort | xargs -I{} -P30 bash -c 'vcfmerger/aux/FastTreeMP -fastest -gamma -nt -bionj -boot 100 -log {}.tree.log -out {}.tree {}'
+            OUTPUT: PROJNAME/CHROMOSOME/short2.lst.vcf.gz.simplified.vcf.gz.filtered.vcf.gz.SL2.40ch01.000090300001-000090310000.Frag_SL2.40ch01g10000_9031.vcf.gz.SL2.40ch01.fasta.tree
+                ((((Dana_018:0.0,Belmonte_033:0.0):0.00054,((TR00026_102:0.01587,(PI272654_023:0.03426,(((S_huaylasense_063:0.00054,((Lycopersicon_sp_025:0.0,S_chilense_065:0.0):0.00054,S_chilense_064:0.01555)0.780:0.01548)0.860:0.01547,((S_peruvianum_new_049:0.0,S_chiemliewskii_051:0.0,S_chiemliewskii_052:0.0,S_cheesemaniae_053:0.0,S_cheesemaniae_054:0.0,S_neorickii_056:0.0,S_neorickii_057:0.0,S_peruvianum_060:0.0,S_habrochaites_glabratum_066:0.0,S_habrochaites_glabratum_068:0.0,S_habrochaites_070:0.0,S_habrochaites_071:0.0,S_habrochaites_072:0.0,S_pennellii_073:0.0,S_pennellii_074:0.0,TR00028_LA1479_105:0.0,ref:0.0):0.00054,((S_arcanum_058:0.01482,(S_huaylasense_062:0.08258,S._arcanum_new_075:0.00054)0.880:0.03260)0.960:0.04917,(((Gardeners_Delight_003:0.00054,(Katinka_Cherry_007:0.0,Trote_Beere_016:0.0,Winter_Tipe_031:0.0):0.01559)0.900:0.03206,(PI129097_022:0.00054,(S_galapagense_104:0.04782,(LA0113_039:0.01223,((S_pimpinellifolium_047:0.01628,(S_arcanum_059:0.00055,(S_habrochaites_glabratum_067:0.01562,S_habrochaites_glabratum_069:0.01562)1.000:0.08287)0.920:0.04857)0.670:0.01186,S_habrochaites_042:0.03551)0.990:0.12956)0.960:0.06961)0.710:0.00054)0.800:0.01578)0.760:0.01558,(T1039_017:0.08246,S_pimpinellifolium_044:0.00054)0.980:0.08153)0.230:0.00053)0.910:0.00055)0.910:0.00054)0.830:0.01549,S_pimpinellifolium_046:0.00054)0.980:0.08610)0.660:0.01369)0.530:0.04644,(TR00027_103:0.00054,(PI365925_037:0.04936,S_cheesemaniae_055:0.03179)0.650:0.08462)1.000:0.41706)0.650:0.00296)0.940:0.01555,(The_Dutchman_028:0.00053,(((Polish_Joe_026:0.0,Brandywine_089:0.0):0.00054,((((Porter_078:0.01608,Kentucky_Beefsteak_093:0.01542)0.880:0.03271,(Thessaloniki_096:0.08543,Bloodt_Butcher_088:0.03267)0.700:0.01564)0.800:0.01585,(Giant_Belgium_091:0.01562,(Moneymaker_001:0.00054,(Dixy_Golden_Giant_090:0.01579,(Large_Red_Cherry_077:0.03276,Momatero_015:0.04969)0.720:0.01528)0.870:0.01570)0.850:0.01556)0.480:0.00055)0.930:0.03157,Marmande_VFA_094:0.03158)0.970:0.00053)0.880:0.00053,Watermelon_Beefsteak_097:0.01555)0.890:0.01559)0.970:0.03159)0.950:0.00054,PI169588_041:0.00054,((Sonato_012:0.11798,(((All_Round_011:0.01555,Chih-Mu-Tao-Se_038:0.00054)0.180:0.00054,(((Jersey_Devil_024:0.0,Chag_Li_Lycopersicon_esculentum_032:0.0,S_pimpinellifolium_unc_043:0.0):0.00054,(((PI311117_036:0.04839,((Taxi_006:0.0,Tiffen_Mennonite_034:0.0):0.00054,(Cal_J_TM_VF_027:0.00053,(Lycopersicon_esculentum_828_021:0.00054,(Black_Cherry_029:0.03245,(Galina_005:0.00054,S_pimpinellifolium_unc_045:0.01559)0.880:0.03248)0.770:0.01547)0.950:0.03179)0.160:0.01560)0.840:0.01563)0.420:0.00054,Lycopersicon_esculentum_825_020:0.00054)0.860:0.01556,((Cross_Country_013:0.0,ES_58_Heinz_040:0.0):0.00054,(Rutgers_004:0.01554,Lidi_014:0.04758)0.900:0.00054)0.880:0.00054)0.860:0.01558)0.080:0.01560,(Alisa_Craig_002:0.01560,John_s_big_orange_008:0.00054)1.000:0.00054)0.840:0.01558)0.800:0.01566,(Large_Pink_019:0.01555,Anto_030:0.00054)0.140:0.00054)0.920:0.01555)0.680:0.00054,Wheatley_s_Frost_Resistant_035:0.03155)0.950:0.00054);
+
+        find PROJNAME -name '*.fasta' | sort | xargs -I{} -P30 bash -c 'vcfmerger/aux/FastTreeMP -nt -makematrix {} > {}.matrix'
+            OUTPUT: PROJNAME/CHROMOSOME/short2.lst.vcf.gz.simplified.vcf.gz.filtered.vcf.gz.SL2.40ch01.000090300001-000090310000.Frag_SL2.40ch01g10000_9031.vcf.gz.SL2.40ch01.fasta.matrix
+                Moneymaker_001 0.000000 0.134437 0.345611 0.134437  0.321609
+                Alisa_Craig_002 0.134437 0.000000 0.211925 0.064210
+                Gardeners_Delight_003 0.345611 0.211925 0.000000 0.211925
+
+
+
+    Process the data into memory dump database (pyckle):
+        vcf_walk_ram.py --pickle PROJNAME
+            OUTPUT:
+                walk_out_10k.db
+                walk_out_10k_SL2.40ch00.db
+                walk_out_10k_SL2.40ch01.db
+                walk_out_10k_SL2.40ch02.db
+                walk_out_10k_SL2.40ch03.db
+                walk_out_10k_SL2.40ch04.db
+                walk_out_10k_SL2.40ch05.db
+                walk_out_10k_SL2.40ch06.db
+                walk_out_10k_SL2.40ch07.db
+                walk_out_10k_SL2.40ch08.db
+                walk_out_10k_SL2.40ch09.db
+                walk_out_10k_SL2.40ch10.db
+                walk_out_10k_SL2.40ch11.db
+                walk_out_10k_SL2.40ch12.db
+
+
+    Convert (pickle) database to SQLite (if dependencies installed):
+        vcf_walk_sql.py PROJNAME
+            OUTPUT:
+                walk_out_10k.sql.db
+
+
+5.2. Server
+    Run vcf_walk_server.py
+
+    Run svg_server.py (if dependencis are installed)
+
+    Run cluster_server.py (if dependencis are installed)
+
+
+
+
+6. Acknowledgements
+Sander Peters
+Hans de Jong
+Gabino Perez

config.py

+import os
+bin_path = os.path.abspath( __file__ )
+dir_path = os.path.dirname( bin_path )
+
+#decide whether to have user control or not
+hasLogin    = False
+
+#add credentials
+credentials = {
+	'xxx'   : 'yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy',
+}
+
+
+#to create passwords, in the command line, run python in interactive mode and type:
+#import hashlib
+#hashlib.sha256("<LOGIN><PASSWORD>").hexdigest()
+
+
+
+#define port. cluster server and svg server will use this port +1 and +2, respectively
+SERVER_PORT               = 10000
+
+
+#define if uses SQL or RAM database
+USE_SQL                   = True
+
+
+#define cookie security key. if not changed anyone who knows this code can login
+SECRET_KEY                = "development key"
+SECRET_KEY                = '91\xba\xf0+R\xbd\x14_\xcb\xa9\xd9\xd7\xdb\xb4\xbcTK \x9d(PL\xb0'
+
+#to create a new security key, in the command line, run python in interactive mode and type:
+#import os
+#os.urandom(24)
+#'\xe1:\xbf\xc2\xaa\x0b\x04\xb8\xac\xc1\xff;Z-W\xfcRE\xadY"K\xa1v'
+
+
+#define available databases
+#DATABASES = [
+#    [ 'Solanum 60 RIL Moneymaker vs pimpinellifolium'                    , 'data/walk_out_ril'       ],
+#    [ 'Solanum 60 RIL Moneymaker vs pimpinellifolium w parents'          , 'data/walk_ril_parent'    ],
+#    [ 'Solanum 60 RIL Moneymaker vs pimpinellifolium w parents no gaps 1', 'data/walk_ril_3_nogaps'  ],
+#    [ 'Solanum 60 RIL Moneymaker vs pimpinellifolium w parents no gaps 3', 'data/walk_ril_4_nogaps_3'],
+#    [ 'Solanum 84 Genes'                                                 , 'data/walk_out_genes'     ],
+#    [ 'Solanum 84 50 Kbp window'                                         , 'data/walk_out_50k'       ],
+#    [ 'Solanum 84 10 Kbp window'                                         , 'data/walk_out_10k'       ]
+#]
+
+INFOLDER                  = os.path.join( dir_path, "data" )
+
+DEBUG                     = False
+MAX_NUMBER_OF_COLUMNS     = 300
+MAX_CONTENT_LENGTH        = 128 * 1024 * 1024

docker/Dockerfile

+#docker run -it --security-context apparmor:unconfine -v $PWD/data:/var/www/ibrowser/data -v $PWD/access.log:/var/log/apache2/access.log -v $PWD/error.log:/var/log/apache2/error.log ibrowser
+#docker build -t ibrowser .
+
+FROM ubuntu:14.10
+
+RUN apt-get clean all && \
+    apt-get update && \
+    apt-get install -y libapache2-mod-wsgi apache2 nano && \
+    a2enmod wsgi && a2enmod proxy && a2enmod proxy_http && a2enmod rewrite && \
+    sed -ie "s/Listen 80/Listen 8000/" /etc/apache2/ports.conf 
+
+RUN apt-get install -y python-virtualenv libjpeg62 libjpeg62-dev libfreetype6 libfreetype6-dev \
+    zlib1g-dev python-setuptools build-essential zlib1g-dev libjpeg62 libjpeg62-dev \
+    python-pip python-dev python-numpy python-scipy python-matplotlib \
+    python-imaging pkg-config libblas-dev liblapack-dev gfortran && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ADD iBrowser         /var/www/ibrowser
+
+WORKDIR /var/www/ibrowser
+
+#ln -s /var/www/ibrowser/static/       /var/www/html/static && \
+RUN ln -s /var/www/ibrowser/ibrowser.conf /etc/apache2/mods-enabled/ibrowser.conf && \
+    virtualenv venv && \
+    bash -c "source ./venv/bin/activate && \
+    pip install --requirement /var/www/ibrowser/requirements.txt"
+
+VOLUME [ "/var/www/ibrowser/data" ]

docker/run.sh

+touch access.log error.log
+docker run -it --security-opt="apparmor:unconfine" \
+-v $PWD/data:/var/www/ibrowser/data \
+-v $PWD/access.log:/var/log/apache2/access.log \
+-v $PWD/error.log:/var/log/apache2/error.log \
+--hostname="assembly.ab.wurnet.nl" \
+ibrowser
+

ibrowser.conf

+ServerName assembly.ab.wurnet.nl
+
+<VirtualHost *:8000>
+ServerAdmin sauloalves.aflitos@wur.nl
+
+#ServerName ibrowser.assembly.ab.wurnet.nl
+#ServerAlias *.ibrowser.assembly.ab.wurnet.nl
+
+DocumentRoot /var/www/ibrowser
+
+RewriteEngine On
+ProxyPreserveHost On
+
+# Tells apache where /static/ should go
+Alias /static/ /var/www/ibrowser/static/
+
+ProxyPass /favicon.ico !
+ProxyPass /static !
+
+ProxyPass         / http://localhost:10000/
+ProxyPassReverse  / http://localhost:10000/
+
+LogLevel debug
+
+</VirtualHost>
+

ibrowser.conf2

+#<VirtualHost *>
+
+WSGIDaemonProcess   ibrowser user=www-data group=www-data threads=5
+WSGIScriptAlias    /ibrowser /var/www/ibrowser/ibrowser.wsgi
+WSGIRestrictStdout Off
+
+<Directory /var/www/ibrowser>
+  WSGIProcessGroup     ibrowser
+  WSGIApplicationGroup %{GLOBAL}
+  Order deny,allow
+  Allow from all
+</Directory>
+
+Alias /static /var/www/ibrowser/static
+<Directory /var/www/ibrowser/static/>
+  Order allow,deny
+  Allow from all
+</Directory>
+
+#</VirtualHost>
+
+LogLevel debug

ibrowser.wsgi

+ibrowser.py
\ No newline at end of file

install.ubuntu.sh

+apt-get install -y python-setuptools build-essential libfreetype6 libfreetype6-dev zlib1g-dev libjpeg62 libjpeg62-dev python-pip python-dev python-numpy python-scipy python-matplotlib python-imaging pkg-config libblas-dev liblapack-dev gfortran apache2
+
+a2enmod wsgi
+
+easy_install --user flask
+easy_install --user ete2
+easy_install --user PIL
+easy_install --user Image
+easy_install --user sqlalchemy
+
+ln -s ibrowser.conf /etc/apache2/mods-available/ibrowser.conf

install.virtualenv.sh

+Howto install (with virtualenv) :
+
+git clone ssh://assembly@assembly.ab.wurnet.nl:/home/assembly/tomato150/programs/iBrowser
+
+apt-get install python-virtualenv libjpeg62{,-dev} libfreetype6 libfreetype6{,-dev} zlib1g-dev python-setuptools build-essential libfreetype6 libfreetype6-dev zlib1g-dev libjpeg62 libjpeg62-dev python-pip python-dev python-numpy python-scipy python-matplotlib python-imaging pkg-config libblas-dev liblapack-dev gfortran apache2
+
+a2enmod wsgi
+
+virtualenv venv && source ./venv/bin/activate
+
+cat requirements.txt
+flask
+ete2
+Pillow
+Image
+sqlalchemy
+numpy
+scipy
+matplotlib
+#MySQL-python
+
+
+pip install --requirement requirements.txt #(takes a while)
+
+cd data && scp -c arcfour assembly@assembly:/home/assembly/tomato150/programs/iBrowser/iBrowser.data.tar.gz . && tar xvzf iBrowser.data.tar.gz && rm iBrowser.data.tar.gz && cd - python ibrowser.py
+
+ln -s ibrowser.conf /etc/apache2/mods-available/ibrowser.conf

mkbackup.sh

+export GZIP=-1
+
+tar acvf iBrowser.code.tar.gz static/ vcfmerger/ *.sh *.bat *.py *.md
+
+cd data
+tar acvf ../iBrowser.data.tar.gz *.sqlite *.nfo *.customorder
+
+
+
+

mkwin.sh

+OUTFILE=introgression_viewer.tgz
+INFOLDER=win
+
+rm $OUTFILE
+rm $INFOLDER/*.*
+rm -rf $INFOLDER/static
+
+cp -l   *.py            $INFOLDER
+cp -l   walk_out.sql.db $INFOLDER
+cp -l   run.bat         $INFOLDER
+cp -lar static          $INFOLDER
+
+tar --exclude '*.pyc' --totals --level 9 -cvSzf $OUTFILE $INFOLDER
+
+rm $INFOLDER/*.*
+rm -rf $INFOLDER/static

requirements.txt

+flask
+ete2
+sqlalchemy
+##if not in the system
+#Pillow
+#Image
+#numpy
+#scipy
+#matplotlib
+#MySQL-python
+

restarter.sh

+RUNNING=`ps aux | grep ibrowser.py | grep -v grep | wc -l`
+
+if [[ "$RUNNING" == "0" ]]; then
+	echo "NOT RUNNING. STARTING AGAIN"
+	
+else
+	echo "ALREADY RUNNING"
+fi

run.bat

+python vcf_walk_server.py walk_out

static/css/custom.css

+html {
+    background-color: #fff;
+}
+
+body {
+    background-color: #fff;
+    font-size: 13px;
+    font-family: FontAwesome, proxima-nova, "Helvetica neue", Helvetica, Arial, Freesans, sans-serif;
+    margin-top: 2em;
+    width: 100%;
+    /*overflow: scroll;*/
+    /*overflow-x: scroll;*/
+    /*overflow-y: scroll;*/
+
+    /*-webkit-border-radius: 10px;*/
+    /*   -moz-border-radius: 10px;*/
+    /*        border-radius: 10px;*/
+    /*color: #444;*/
+    /*background-color: #fff;*/
+    /*padding: 1em 1em;*/
+    /*width: 95%;*/
+    /*height: 99%;*/
+    /*margin: 5% auto;*/
+    /*box-shadow:				1px 1px 8px #444;*/
+    /*-mox-box-shadow:		1px 1px 8px #444;*/
+    /*-webkit-box-shadow:		1px -1px 8px #444;*/
+    /*visibility: hidden;*/
+}
+
+#wrap {
+    position: absolute;
+    top: 4em;
+    left: 0px;
+    width: 100%;
+    z-index: 90;
+}
+
+#wrap_svg {
+    overflow: scroll;
+    overflow-x: scroll;
+    overflow-y: scroll;
+}
+
+#status {
+    position: fixed;
+    top: 0px;
+    left: 10%;
+    width: 100%;
+    height: 2em;
+    background: #093;
+    color: white;
+    z-index: 100;
+}
+
+.status_div{
+    float: left;
+}
+
+#wrap_buttons {
+    position: fixed;
+    top: 2em;
+    left: 10%;
+    width: 100%;
+    height: 2em;
+    display: block;
+    color: white;
+    background: #093;
+    z-index: 100;
+}
+
+#main_col {
+    top: 0px;
+    left: 0px;
+    position: fixed;
+    width: 10%;
+    height: 4em;
+    overflow: hidden !important;
+    float: right;
+    text-align: left;
+	white-space: nowrap;
+    background: #080;
+    color: white;
+    z-index: 100;
+}
+
+#main_col:hover {
+    width: 40em;
+    height: 100%;
+    display: block;
+    z-index: 1000;
+}
+
+.main_col_setup {
+    height: 4em;
+}
+
+.main_col_div {
+    width: 40em;
+}
+
+#footer {
+    color: black;
+    background: #f2f2f2;
+}
+
+#imgcanvas{
+    position: absolute;
+    top: 4em;
+}
+
+img {