Recent changes to Home

Home modified by Laboratório de Biodados

Laboratório de Biodados — Sun, 14 May 2017 11:42:46 -0000

--- v17
+++ v18
@@ -28,7 +28,7 @@
 BOWS requires MySQL. To install MySQL in a UNIX platform, follow these steps:
 For **Fedora**, **CentOS** or **RedHat** operating systems, type the following command to download and install MySQL:

-   > su -c “yum install mysql mysql-server“
+   > sudo yum install mysql mysql-server

 For **Debian** or **Ubuntu** operating systems, use this command:

@@ -62,100 +62,20 @@

     > sudo apt-get install openjdk-7-jre

-**Fedora, Oracle Linux, Red Hat Enterprise Linux, etc.**
-
-    > su -c “yum install java-1.7.0-openjdk”
+**Fedora, Oracle Linux, Red Hat Enterprise Linux, CentOS, etc.**
+
+    > sudo yum install java-1.7.0-openjdk

 ####2.1.3. Apache Tomcat####

-To install Tomcat simple download, extract the archive and start the tomcat server.
-We recommend install Apache Tomcat into /usr/local/ folder, to do this log in as root typing in the Terminal:  
-
-   > su
-   
-Then go to directory /usr/local by typing in the Terminal:
-
-   > cd /usr/local/
-   
-After that download Apache Tomcat7 typing:
-
-   > wget http://ftp.unicamp.br/pub/apache/tomcat/tomcat-7/v7.0.57/bin/apache-tomcat-7.0.57.tar.gz
-   
-Decompress the file typing the following command:
-   
-   > tar xvzf apache-tomcat-7.0.57.tar.gz
-   
-And finally start tomcat:
-
-   > cd apache-tomcat-7.0.57
-   > bin/startup.sh
-   
-To configure Tomcat as service type the following commands:
-Change to the /etc/init.d directory and create a script called 'tomcat' as shown below:
-
-   > cd /etc/init.d/
-   > vi tomcat
-   
-Attention to copy this script, check if JAVA_HOME folder is correct:
-
-   #!/bin/bash  
-   # description: Tomcat Start Stop Restart  
-   # processname: tomcat  
-   # chkconfig: 234 20 80  
-   JAVA_HOME=/usr/lib/java-1.7.0/
-   export JAVA_HOME  
-   PATH=$JAVA_HOME/bin:$PATH  
-   export PATH  
-   CATALINA_HOME=/usr/local/apache-tomcat-7.0.57 
-     
-   case $1 in  
-   start)  
-   sh $CATALINA_HOME/bin/startup.sh  
-   ;;   
-   stop)     
-   sh $CATALINA_HOME/bin/shutdown.sh  
-   ;;   
-   restart)  
-   sh $CATALINA_HOME/bin/shutdown.sh  
-   sh $CATALINA_HOME/bin/startup.sh  
-   ;;   
-   esac      
-   exit 0
-   
-Then change file permission:
-
-   > chmod 755 tomcat
-   
-Now use the chkconfig utility to have Tomcat start at boot time typing the commands:
-   
-   > chkconfig --add tomcat
-   > chkconfig --level 234 tomcat on 
-
-Tomcat by default start on port 8080. To allow access in this port edit iptables. Log in as root, then type:
-
-    > vi /etc/sysconfig/iptables
-
-Press key "i" to edit  
-Add this following line above the "-A INPUT -j REJECT" lines: 
-    -A INPUT -p tcp -m state --state NEW -m tcp --dport 8080 -j ACCEPT 
-Iptables should have something like this:
-
-   :INPUT ACCEPT [0:0]
-   :FORWARD ACCEPT [0:0]
-   :OUTPUT ACCEPT [4:464]
-   -A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-   -A INPUT -p icmp -j ACCEPT
-   -A INPUT -i lo -j ACCEPT
-   -A INPUT -p tcp -m state --state NEW -m tcp --dport 22 -j ACCEPT
-   -A INPUT -p tcp -m state --state NEW -m tcp --dport 8080 -j ACCEPT
-   -A INPUT -j REJECT --reject-with icmp-host-prohibited
-   -A FORWARD -j REJECT --reject-with icmp-host-prohibited
-   COMMIT
-
-To close and save alterations press "Esc" then ":x!"
-After that, restart iptables typing the command:
-
-   > /etc/init.d/iptables restart
+To install Tomcat  type on Terminal the following command line according to your Unix distribution: 
+**Debian, Ubuntu, etc.**
+
+    > sudo apt-get install tomcat7
+
+**Fedora, Oracle Linux, Red Hat Enterprise Linux, CentOS, etc.**
+
+    > sudo yum install tomcat 

 ###2.2. Downloading BOWS###

@@ -188,7 +108,7 @@

 To install the BOWS service, copy the file "BOWS.war" file into "webapps" folder of Apache Tomcat:

-    > cp BOWS.war /usr/local/apache-tomcat-7.0.57/webapps/
+    > cp BOWS.war /usr/share/tomcat/webapps/

 Then restart the tomcat service by typing:

@@ -381,6 +301,8 @@

 ##6. Troubleshooting##

+###6.1###
+
 If you experience some problems with clients presenting the message:

     "could not roll back hibernate transaction; nested exception is org.hibernate.transactionexception: jdbc rollback failed" 
@@ -388,6 +310,12 @@
 Try to restart your tomcat service to fix it.

     > service tomcat restart
+
+###6.2###
+
+If you are having problems of disk usage by some tomcat files, try the command below:
+
+    > mv /etc/tomcat/logging.properties /etc/tomcat/logging.properties_OFF

 ##7. License##

Home modified by Laboratório de Biodados

Laboratório de Biodados — Thu, 19 Mar 2015 13:26:03 -0000

--- v16
+++ v17
@@ -326,15 +326,9 @@

     > java -jar Arrow_yourapp.jar pathtoapp/

-We recommend to register the arrow on crontab to start every time that the server reboots.
-
-To edit your crontab use the command:
-
-    > crontab -e
-
-Then add the line relative to the application:
-
-    @reboot cd /pathtoapp/ && java -jar Arrow_yourapp.jar /pathtoapp/ &> /dev/null
+We recommend to register the arrow on crontab. To add to your crontab just run the script:
+
+    ./add_to_crontab.sh

 ####4.2.2. Front-end auto-generated clients####

Home modified by Laboratório de Biodados

Laboratório de Biodados — Mon, 22 Dec 2014 15:39:12 -0000

--- v15
+++ v16
@@ -20,7 +20,7 @@

 * UNIX platform;
 * MySQL;
-* Java;
+* Java 1.7;
 * Apache Tomcat.

 ####2.1.1. MySQL####
@@ -218,7 +218,7 @@
     ApplicationParamConfig[] parametersList  = new ApplicationParamConfig[1];
     parametersList[0] = parameters;
     // Create app
-    service.createApplication("App Code", "App Name", "App Description", parametersList);
+    service.createApplication("Author Code", "App Code", "App Name", "App Description", parametersList);

 ###3.2. Back-end###

@@ -229,7 +229,7 @@
     BOWSAdminServicePortTypeProxy service = new BOWSAdminServicePortTypeProxy();
     // Retrieve process information
     ProcessDetailsResponse toRun = new ProcessDetailsResponse();
-    toRun = service.nextQueuedProcess("App Code", true);
+    toRun = service.nextQueuedProcess("Author Code", "App Code", true);
     long processId = toRun.getProcessId();
     SubmissionParam[] params = new SubmissionParam[1];
     params = toRun.getParams();
@@ -247,7 +247,7 @@
     response = service.insertProcessResult(result);
     System.out.println(response.getMessage());
     // Change status
-    response = service.changeProcessStatus(processId, "App Code", ProcessStatus.FINISHED , "No Error");
+    response = service.changeProcessStatus("Author Code", processId, "App Code", ProcessStatus.FINISHED , "No Error");

 ###3.3. Front-end###

@@ -267,7 +267,7 @@
     submitProcessParamArray[0] = submitProcessParam;       
     // Submit job
     SubmissionResponse submitResponse = new SubmissionResponse();
-    submitResponse = service.submitProcess("App Code",submitProcessParamArray);
+    submitResponse = service.submitProcess("User Code","App Code",submitProcessParamArray);
     // Return process id
     long processId = submitResponse.getProcessId();

@@ -277,14 +277,14 @@
     // Declare webservice object
     BOWSServicePortTypeProxy service = new BOWSServicePortTypeProxy();
     // Check Status
-    if (new String("FINISHED").equals(service.checkProcessStatus(processId).getStatus().toString())){
+    if (new String("FINISHED").equals(service.checkProcessStatus("User Code",processId).getStatus().toString())){
         // Retrieve result
         ProcessResultResponse resultResponse = new ProcessResultResponse();
-   resultResponse = service.getProcessResult(processId);
+   resultResponse = service.getProcessResult("User Code",processId);
    System.out.println(resultResponse.getResultText());
    return;
     }else{
-        System.out.println("Process status: " + service.checkProcessStatus(processId).getStatus().toString());
+        System.out.println("Process status: " + service.checkProcessStatus("User Code",processId).getStatus().toString());
    return;         
     }

@@ -297,13 +297,6 @@
 > cp BOWSWeb.war /usr/local/apache-tomcat-7.0.57/webapps/

 The Apache Tomcat needs to use the default port 8080 for all features work properly. 
-
-To access the administrative functions (register/remove application) use:
-
-    login:admin
-    password:123
-
-To change these credentials, the table "users" in the database "bows" needs to be directly changed. 

 ###4.2. BOWS auto-generated clients###

@@ -331,7 +324,7 @@

 After edit this script save it and let the jar client running on server. The jar receives the path to application as parameter:

-    > java -jar Arrow_yourapp.jar pathtoapp
+    > java -jar Arrow_yourapp.jar pathtoapp/

 We recommend to register the arrow on crontab to start every time that the server reboots.

@@ -341,36 +334,38 @@

 Then add the line relative to the application:

-    @reboot cd /pathtoapp/ && java -jar Arrow_yourapp.jar /pathtoapp &> /dev/null
+    @reboot cd /pathtoapp/ && java -jar Arrow_yourapp.jar /pathtoapp/ &> /dev/null

 ####4.2.2. Front-end auto-generated clients####

 The website also creates the java clients for the end-user. On the application details page, it is available for download the Submit Job and the Get Results clients. The Get Results clients are the same for all applications registered, it receives only the job pid as parameter. To run it in use the command: 

-    > java -jar getresults.jar -pid 111
+    > java -jar getresults.jar -user usercode -pid 111

 A GUI client for the Get Results are also available. Just double click on icon to run.

 The Submit Job client receives the defined parameters and returns to user the job pid. To run it, for example:

-    > java -jar prankSubmitJob.jar -fasta file.fasta
+    > java -jar prankSubmitJob.jar -user usercode -fasta file.fasta

 Attention for the parameter type, if it is registered as binary, the file name must to be used. If is text just pass the values inline.

 ##5. BOWS Client: DEMOS##

-Three BOWS demos registered at http://bioinfo.icb.ufmg.br:8080/BOWS/services are available into file BOWS_DEMO.tar.gz
+Three BOWS demos registered at http://biodados.icb.ufmg.br:8080/BOWS/services are available into file BOWS_DEMO.tar.gz

 To retrieve the result for all demos, run the Get Results client with sending the process id parameter with the flag -pid, as shown below:

-    > java -jar getresults.jar -pid 111
+    > java -jar getresults.jar -user usercode -pid 111
+
+For each one there is also graphical user interface clients, that can be used by just double clicking on jar file.

 ###5.1. Multiple Alignment with PRANK###

 Perform the PRANK multiple alignment remotely using BOWS management.
 A file with sequences for example is available, to use just type:

-    > java -jar prankalignSubmitJob.jar -fasta myoglobins
+    > java -jar prankalignSubmitJob.jar -user usercode -fasta myoglobins

 ###5.2. BLAST on UniProt Complete###

@@ -378,13 +373,13 @@
 BLASTp is configured with e-value of 1e-10 and maximum 200 hits. Results are available on BLAST output tabular format with comment lines with default columns adding the query and subject lengths and query coverage. 

 A file with sequences for example is available, to use just type:
-    > java -jar blastonuekoSubmitJob.jar -fasta sequence.fasta
+    > java -jar blastonuekoSubmitJob.jar -user usercode -fasta sequence.fasta

 ###5.3. Clustering with SeedLinkage###

 SeedLinkage is a method to cluster cognate proteins from multiple organisms beginning with only one sequence, through connectivity saturation with that Seed sequence. To use just type:

-    > java -jar seedserverSubmitJob.jar -seed Q01860,Q10589
+    > java -jar seedserverSubmitJob.jar -user usercode -seed Q01860,Q10589

 The output contain three columns: 
 CLUSTER NUMBER TAX ID SEQUENCE ID

Home modified by Laboratório de Biodados

Laboratório de Biodados — Mon, 17 Nov 2014 17:43:44 -0000

--- v14
+++ v15
@@ -357,11 +357,89 @@

 Attention for the parameter type, if it is registered as binary, the file name must to be used. If is text just pass the values inline.

-##5. BOWS Client: DEMO##
+##5. BOWS Client: DEMOS##
+
+Three BOWS demos registered at http://bioinfo.icb.ufmg.br:8080/BOWS/services are available into file BOWS_DEMO.tar.gz
+
+To retrieve the result for all demos, run the Get Results client with sending the process id parameter with the flag -pid, as shown below:
+
+    > java -jar getresults.jar -pid 111

 ###5.1. Multiple Alignment with PRANK###

-PrankBows.jar perform the PRANK multiple alignment remotely using BOWS management.
+Perform the PRANK multiple alignment remotely using BOWS management.
 A file with sequences for example is available, to use just type:
-java -jar prank.jar myoglobins
-The output is a fasta formatted file named as the input file name followed by '.result'
+
+    > java -jar prankalignSubmitJob.jar -fasta myoglobins
+
+###5.2. BLAST on UniProt Complete###
+
+Performs a BLASTp search on UniProt complete database (Fragment sequences removed). 
+BLASTp is configured with e-value of 1e-10 and maximum 200 hits. Results are available on BLAST output tabular format with comment lines with default columns adding the query and subject lengths and query coverage. 
+
+A file with sequences for example is available, to use just type:
+    > java -jar blastonuekoSubmitJob.jar -fasta sequence.fasta
+
+###5.3. Clustering with SeedLinkage###
+
+SeedLinkage is a method to cluster cognate proteins from multiple organisms beginning with only one sequence, through connectivity saturation with that Seed sequence. To use just type:
+
+    > java -jar seedserverSubmitJob.jar -seed Q01860,Q10589
+
+The output contain three columns: 
+CLUSTER NUMBER TAX ID SEQUENCE ID 
+Cluster number refers to the number of the cluster that this particular sequence belongs, tax id is the taxon id for that same sequence and sequence id is the sequence id provided.
+
+##6. Troubleshooting##
+
+If you experience some problems with clients presenting the message:
+
+    "could not roll back hibernate transaction; nested exception is org.hibernate.transactionexception: jdbc rollback failed" 
+
+Try to restart your tomcat service to fix it.
+
+    > service tomcat restart
+
+##7. License##
+
+**IMPORTANT! READ CAREFULLY: THIS IS A LEGAL AGREEMENT** 
+BOWS Bioinformatics Open Web Services software Copyright © 2014 Henrique Velloso, Ricardo A. Vialle, J. Miguel Ortega. All rights reserved. 
+
+BOWS software development: Henrique Velloso and Ricardo A. Vialle.
+
+Laboratory of Biodados
+Federal University of Minas Gerais Department of Biochemistry 
+Av. Antonio Carlos, 6627, Pampulha 
+Belo Horizonte – MG Brazil 
+
+The BOWS software is only available for download from https://sourceforge.net/projects/bows/ 
+By installing BOWS, you are agreeing to be bound by this agreement ("Agreement"). If you do not agree with all of the terms of this Agreement, reject the Agreement by refusing to install the BOWS software. 
+
+**1) Definitions** 
+
+**1.1)** "DEVs" means the developers and copyright owners of BOWS software, as defined at the beginning of this License Agreement. 
+
+**2) Ownership** 
+
+**2.1)** The Software is owned and copyrighted by DEVs. This Agreement confers no title or ownership in the Software and is not a sale of any rights in the Software. 
+
+**2.2)** This Agreement does not grant you and/or any person(s) acting with you or for you, any rights or license with respect to the source code of the Software. 
+
+**3) Disclaimer of Warranties & Limitation of Liability** 
+
+THE SOFTWARE IS PROVIDED BY DEVs "AS IS" WITHOUT A WARRANTY OF ANY KIND, AND ANY EXPRESS OR IMPLIED 
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL DEVs BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. NO WARRANTY IS MADE THAT THE SOFTWARE WILL MEET YOUR REQUIREMENTS. 
+
+**4) Indemnification** 
+
+You agree to fully indemnify and hold harmless DEVs from and against any and all claims, liabilities, demands, suits, losses, damages, costs, settlement amounts, and/or expenses, including but not limited to attorneys' fees, arising out of your use of the Software. 
+
+The following BSD LICENSE applies to these custom functions only, referred to as "THIS SOFTWARE": 
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 
+
+* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 
+
+* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Home modified by Laboratório de Biodados

Laboratório de Biodados — Sun, 16 Nov 2014 14:01:22 -0000

--- v13
+++ v14
@@ -51,7 +51,7 @@
 Log in as root to create a new user called "bows" and grant permissions to create databases by typing the commands:

     mysql> CREATE USER 'bows'@'localhost' IDENTIFIED BY 'bows123';
-    mysql> GRANT ALL PRIVILEGES ON * . * TO 'bows'@'localhost';
+    mysql> GRANT ALL PRIVILEGES ON bows.* TO 'bows'@'localhost';

 This user account is required by BOWS (see 2.3. Creating and configuring BOWS database).

@@ -79,15 +79,15 @@

 After that download Apache Tomcat7 typing:

-   > wget http://ftp.unicamp.br/pub/apache/tomcat/tomcat-7/v7.0.53/bin/apache-tomcat-7.0.53.tar.gz
+   > wget http://ftp.unicamp.br/pub/apache/tomcat/tomcat-7/v7.0.57/bin/apache-tomcat-7.0.57.tar.gz

 Decompress the file typing the following command:

-   > tar xvzf apache-tomcat-7.0.53.tar.gz
+   > tar xvzf apache-tomcat-7.0.57.tar.gz

 And finally start tomcat:

-   > cd apache-tomcat-7.0.53
+   > cd apache-tomcat-7.0.57
    > bin/startup.sh

 To configure Tomcat as service type the following commands:
@@ -106,7 +106,7 @@
    export JAVA_HOME  
    PATH=$JAVA_HOME/bin:$PATH  
    export PATH  
-   CATALINA_HOME=/usr/local/apache-tomcat-7.0.53 
+   CATALINA_HOME=/usr/local/apache-tomcat-7.0.57 

    case $1 in  
    start)  
@@ -188,7 +188,7 @@

 To install the BOWS service, copy the file "BOWS.war" file into "webapps" folder of Apache Tomcat:

-    > cp BOWS.war /usr/local/apache-tomcat-7.0.53/webapps/
+    > cp BOWS.war /usr/local/apache-tomcat-7.0.57/webapps/

 Then restart the tomcat service by typing:

@@ -288,9 +288,78 @@
    return;         
     }

-##4. BOWS Client: DEMO##
-
-###4.1. Multiple Alignment with PRANK###
+##4. BOWS management interface and clients generator##
+
+###4.1. BOWS Website###
+
+A website to enroll, visualize and remove applications registered in BOWS server is available through the file BOWSWeb.war. Install it in the same server that contains the BOWS.war, through the command:
+
+> cp BOWSWeb.war /usr/local/apache-tomcat-7.0.57/webapps/
+
+The Apache Tomcat needs to use the default port 8080 for all features work properly. 
+
+To access the administrative functions (register/remove application) use:
+
+    login:admin
+    password:123
+
+To change these credentials, the table "users" in the database "bows" needs to be directly changed. 
+
+###4.2. BOWS auto-generated clients###
+
+The website will access the registered applications show their information and create java clients to back-end and front-end for each one.
+
+####4.2.1. Back-end auto-generated clients (Arrow)####
+
+The Arrow client is a executable jar that runs in loop looking for queued jobs to run, then it pass the parameters to a shell script that run the application and save the result into a file with an expected name.
+
+Below there is an example of shell script generated:
+
+    #!/bin/sh
+    # Auto-generated BOWS arrow running script.
+    # Edit this script to run your app.
+    # If output is a TEXT value, write the result as $OUTTXT
+    # If output is a BINARY value, write the result as $OUTBIN
+    OUTTXT="${1}_out.txt"
+    OUTBIN="${1}_out.bin"
+    input=$2
+    # Write below your app running command
+
+This script needs to be edit adding the command line that executes the application passing the parameters and sending the result to one of the output files ($OUTTXT for TEXT value result or $OUTBIN for BINARY value result), for example:
+
+    ./run_app $input > $OUTTXT
+
+After edit this script save it and let the jar client running on server. The jar receives the path to application as parameter:
+
+    > java -jar Arrow_yourapp.jar pathtoapp
+
+We recommend to register the arrow on crontab to start every time that the server reboots.
+
+To edit your crontab use the command:
+
+    > crontab -e
+
+Then add the line relative to the application:
+
+    @reboot cd /pathtoapp/ && java -jar Arrow_yourapp.jar /pathtoapp &> /dev/null
+
+####4.2.2. Front-end auto-generated clients####
+
+The website also creates the java clients for the end-user. On the application details page, it is available for download the Submit Job and the Get Results clients. The Get Results clients are the same for all applications registered, it receives only the job pid as parameter. To run it in use the command: 
+
+    > java -jar getresults.jar -pid 111
+
+A GUI client for the Get Results are also available. Just double click on icon to run.
+
+The Submit Job client receives the defined parameters and returns to user the job pid. To run it, for example:
+
+    > java -jar prankSubmitJob.jar -fasta file.fasta
+
+Attention for the parameter type, if it is registered as binary, the file name must to be used. If is text just pass the values inline.
+
+##5. BOWS Client: DEMO##
+
+###5.1. Multiple Alignment with PRANK###

 PrankBows.jar perform the PRANK multiple alignment remotely using BOWS management.
 A file with sequences for example is available, to use just type:

Home modified by Laboratório de Biodados

Laboratório de Biodados — Wed, 27 Aug 2014 16:42:57 -0000

Home modified by Laboratório de Biodados

Laboratório de Biodados — Wed, 27 Aug 2014 16:42:24 -0000

--- v11
+++ v12
@@ -294,5 +294,5 @@

 PrankBows.jar perform the PRANK multiple alignment remotely using BOWS management.
 A file with sequences for example is available, to use just type:
-java -jar PrankBows.jar myoglobins.pep
+java -jar prank.jar myoglobins
 The output is a fasta formatted file named as the input file name followed by '.result'

Home modified by Laboratório de Biodados

Laboratório de Biodados — Wed, 27 Aug 2014 16:36:24 -0000

--- v10
+++ v11
@@ -57,7 +57,7 @@

 ####2.1.2. Java####

-The main code of MaLe-PSI-BLAST was developed in Java (v.1.6.0). To install Java type on Terminal the following command line according to your Unix distribution: 
+To install Java type on Terminal the following command line according to your Unix distribution: 
 **Debian, Ubuntu, etc.**

     > sudo apt-get install openjdk-7-jre
@@ -68,32 +68,7 @@

 ####2.1.3. Apache Tomcat####

-To install Tomcat simple download, extract the archive and start the tomcat server. Tomcat by default start on port 8080. To allow access in this port edit iptables. Log in as root, then type:
-
-    > vi /etc/sysconfig/iptables
-
-Press key "i" to edit  
-Add this following line above the "-A INPUT -j REJECT" lines: 
-    -A INPUT -p tcp -m state --state NEW -m tcp --dport 8080 -j ACCEPT 
-Iptables should have something like this:
-
-   :INPUT ACCEPT [0:0]
-   :FORWARD ACCEPT [0:0]
-   :OUTPUT ACCEPT [4:464]
-   -A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-   -A INPUT -p icmp -j ACCEPT
-   -A INPUT -i lo -j ACCEPT
-   -A INPUT -p tcp -m state --state NEW -m tcp --dport 22 -j ACCEPT
-   -A INPUT -p tcp -m state --state NEW -m tcp --dport 8080 -j ACCEPT
-   -A INPUT -j REJECT --reject-with icmp-host-prohibited
-   -A FORWARD -j REJECT --reject-with icmp-host-prohibited
-   COMMIT
-
-To close and save alterations press "Esc" then ":x!"
-After that, restart iptables typing the command:
-
-   > /etc/init.d/iptables restart
-   
+To install Tomcat simple download, extract the archive and start the tomcat server.
 We recommend install Apache Tomcat into /usr/local/ folder, to do this log in as root typing in the Terminal:  

    > su
@@ -156,6 +131,32 @@
    > chkconfig --add tomcat
    > chkconfig --level 234 tomcat on 

+Tomcat by default start on port 8080. To allow access in this port edit iptables. Log in as root, then type:
+
+    > vi /etc/sysconfig/iptables
+
+Press key "i" to edit  
+Add this following line above the "-A INPUT -j REJECT" lines: 
+    -A INPUT -p tcp -m state --state NEW -m tcp --dport 8080 -j ACCEPT 
+Iptables should have something like this:
+
+   :INPUT ACCEPT [0:0]
+   :FORWARD ACCEPT [0:0]
+   :OUTPUT ACCEPT [4:464]
+   -A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
+   -A INPUT -p icmp -j ACCEPT
+   -A INPUT -i lo -j ACCEPT
+   -A INPUT -p tcp -m state --state NEW -m tcp --dport 22 -j ACCEPT
+   -A INPUT -p tcp -m state --state NEW -m tcp --dport 8080 -j ACCEPT
+   -A INPUT -j REJECT --reject-with icmp-host-prohibited
+   -A FORWARD -j REJECT --reject-with icmp-host-prohibited
+   COMMIT
+
+To close and save alterations press "Esc" then ":x!"
+After that, restart iptables typing the command:
+
+   > /etc/init.d/iptables restart
+
 ###2.2. Downloading BOWS###

 BOWS is available at https://sourceforge.net/projects/bows/files/latest/download
@@ -167,7 +168,7 @@

 BOWS is configured to access MySQL as user "bows" with password "bows123" (see section MySQL in Requirements). To create and fill a MySQL database for BOWS usage, follow this procedures:

-####2.3.1. Creating a database for MaLe-PSI-BLAST####
+####2.3.1. Creating a database for BOWS####

 Open a Terminal and access the bows account on MySQL by typing the command:

@@ -175,23 +176,23 @@

 In the MySQL environment, create a database named bows by typing this command:

-   mysql> create database bows;
+    mysql> create database bows;

 ####2.3.2. Populating the database####

 The file "bows.sql" corresponds to the database dump. To restore the tables into database, type the following command in the Terminal:

-   > mysql --user=bows --password=bows123 bows < bows.sql
+    > mysql --user=bows --password=bows123 bows < bows.sql

 ###2.4. Installing BOWS###

 To install the BOWS service, copy the file "BOWS.war" file into "webapps" folder of Apache Tomcat:

-   > cp BOWS.war /usr/local/apache-tomcat-7.0.53/webapps/
+    > cp BOWS.war /usr/local/apache-tomcat-7.0.53/webapps/

 Then restart the tomcat service by typing:

-   > service tomcat restart
+    > service tomcat restart

 After that BOWS will be working at address http://localhost:8080/BOWS/
 WSDL descriptions will be available at: http://localhost:8080/BOWS/services/BOWS?wsdl and http://localhost:8080/BOWS/services/BOWSAdmin?wsdl
@@ -295,4 +296,3 @@
 A file with sequences for example is available, to use just type:
 java -jar PrankBows.jar myoglobins.pep
 The output is a fasta formatted file named as the input file name followed by '.result'
-

Home modified by Laboratório de Biodados

Laboratório de Biodados — Mon, 07 Jul 2014 21:28:20 -0000

--- v9
+++ v10
@@ -291,7 +291,7 @@

 ###4.1. Multiple Alignment with PRANK###

-PrankBowsFrontend.jar perform the PRANK multiple alignment remotely using BOWS management.
+PrankBows.jar perform the PRANK multiple alignment remotely using BOWS management.
 A file with sequences for example is available, to use just type:
 java -jar PrankBows.jar myoglobins.pep
 The output is a fasta formatted file named as the input file name followed by '.result'

Home modified by Laboratório de Biodados

Laboratório de Biodados — Mon, 07 Jul 2014 21:27:58 -0000

--- v8
+++ v9
@@ -3,6 +3,7 @@

 #### Authors: ####
 * Henrique Velloso 
+* Ricardo A Vialle
 * J Miguel Ortega

@@ -292,6 +293,6 @@

 PrankBowsFrontend.jar perform the PRANK multiple alignment remotely using BOWS management.
 A file with sequences for example is available, to use just type:
-java -jar PrankBowsFrontend.jar prank_test.fas
+java -jar PrankBows.jar myoglobins.pep
 The output is a fasta formatted file named as the input file name followed by '.result'