1. About the Search Launcher Batch Client
2. Search Launcher Batch Client for Unix
3. Search Launcher Batch Client for Windows 95/98/NT
4. Search Launcher Batch Client for Mac
5. Searches using GI or Accession number
6. Download the Search Launcher Batch Client

The Search Launcher Batch Client (SLBC) will read-in multiple input files, perform a specified search (e.g., BLAST, BEAUTY) on each sequence (one at a time), then store the result files on the user's system as individual HTML documents. The search results can then be viewed using Netscape, MS Internet Explorer or another HTML viewer.

The search results will be the same as if the search was performed from our Search Launcher Web Pages except the batch client will

1. automatically read multiple sequences from one or more files (no need to paste the sequences one at a time),
2. run the searches in the background (so that one can log-off if running on a public terminal), and
3. store the result files directly in a user's Mac or Unix directory (no need to do individual saves).

The advantages of this system compared to Email server interfaces, such as mailfasta and msu are:

1. search results are returned as HTML documents with embedded hypertext links to additional information resources, rather than as simple text files,
2. search results are deposited directly into one's directory and do not have to be individually sorted and saved out of one's Email system, and
3. the list of available search and analysis methods (BLAST, BEAUTY, CLUSTAL-W, GRAIL, etc) is always current since it is automatically obtained from the BCM Server each time the batch client is run.

Features of version 2.8 of the Batch Client

1. Minor fixes to use the new server and port
   • http://searchlauncher.bcm.tmc.edu:80/
   • search list and batch client versions now match
2. Starting with version 2.8 search list and batch client versions now match

1. Supports two new types of input formats:
   • lists of sequence IDs and
   • files submitted search results.
2. Support for lists of sequence IDs allows us to offer sequence retrieval, where the sequence file for each sequence ID is retrieved and stored automatically in a user's directory, in fasta format, ready for further sequence analysis.
3. Support for files of submitted search results allows us to offer BEAUTY post-processing for submitted BLASTP and BLASTX search results. So all of the additional BEAUTY information, including the summary figures showing the relative locations of hits, and links to additional information can be added to any protein database search. For best results using this service, see the notes in the Frequently Asked Questions file.
4. For the MS Windows version, the display presents only 15 searches at a time. Hit enter, and the next page will be displayed.

The list of available search and analysis methods for these new types of input formats is also obtained from the BCM server each time the batch client is run. So addition services which require these types of input can be added in the future, without requiring new versions of the Batch Client to be released.

The batch client consists of a single perl script. This script will run on Unix systems, Windows systems, and Macs. A direct network connection to the Internet is required. All systems require perl (version 5 or higher) to be installed prior to the installation of the batch client.

Before installing this software it is best to check if it is already installed.

1. System Requirements
   Perl version 5 or higher (you can check by typing 'perl -v'). If not, then you will have to install perl first. Installing perl will require some time and disk space. Consider asking your system manager or other knowledgeable person for advice. Check our downloads page for a link to the latest version.
   
   
2. How to check if the batch client is already installed
   Try typing 'search-launcher -v'. If the commands prints out version information then it is already installed. Otherwise you will likely get a message containing 'command not found'.
   
   
3. How to install the batch client
   To install the batch client on a Unix system ftp the file search-launcher-2.8.pl or the latest version to the filename search-launcher in a directory in your PATH. Then change the permissions accordingly, being certain to set execute permissions.
   Assuming you want to install the software in the directory /usr/local/bin then:
   • use Netscape or MS Internet Explorer to open the URL ftp://ftp.hgsc.bcm.tmc.edu/sl/software/search-launcher/search-launcher-2.8.pl,
   • save the document as search-launcher-2.8.pl,
   • then run the command 'chmod 755 search-launcher-2.8.pl'.
   • Check to see if it is working by running 'search-launcher-2.8.pl -v' to print the version of the command and 'search-launcher-2.8.pl -h' for help.
     
   
   
4. How to run the batch client under unix
   
   • Change the Perl path.
     Before you run, change the header of the batch client perl script to your perl path:
     #!/your_perl_path/perl
     
     
   • Start the Search Launcher.
     Assume the batch client is installed as above, run command:
     >search-launcher.
     
     
   • Select the type of sequence, protein or dna.
     

     Enter type of sequence ([protein seq(s)]/dna seq(s)/output file(s)/seq ID file(s)):

     The default is protein. A list of searches will display:
     

     General protein sequence/pattern searches:
     1  BLASTP+BEAUTY / nr protein - NCBI's Gapped BLASTP with
        BCM's BEAUTY post-processing - NCBI/BCM (beauty_nr)
     2  BLASTP+BEAUTY / nr protein - NCBI's BLASTP
        with BCM's BEAUTY post-processing - NCBI/BCM (beauty_nr_un)
     3  WU-BLASTP+BEAUTY / nr protein - WU-BLAST 2.0 with gapped alignments &
        BEAUTY post-processing - WU/BCM (blast2p_b)
     	       

   • Select the search:

     Enter number or name of search (? for help):

     There are two ways to run the searches:
     • Type in the search number you want to run. For example, 1 for BLASTP+BEAUTY / nr protein.
     • Another way is to use the program name which is at the end of of each searches. For example, beauty_nr for BLASTP+BEAUTY / nr protein search.
     
     
   • Input sequence file(s):

     Enter file name (wildcard okay, return when done):
     	       

     You can have multiple inputs. For each correct input files, the batch client will tell you the files that have been selected. Hit enter twice after the last input.
     
     
   • Submit search
     After entering all sequence files and hitting enter, you searches will be submitted to the Search Launcher web server automatically. You will see a message:
     

     	       Submitting searches as background task, check the file search-launcher.log
     	       

     View the file search-launcher.log to see if there are any problems with the search. The final results will be stored in the directory where you run the search-launcher command.

1. System Requirements
   Perl version 5 or higher (you can check by starting a DOS window and typing 'perl -v' then hit <enter> If the commands prints out version information then it is already installed. Otherwise you will likely get a message containing 'command not found'.) If not, then you will have to install perl first. Installing perl will require some time and disk space. Consider asking your system manager or other knowledgeable person for advice. Check our downloads page for a link to the latest version.
   
   
2. How to check if the batch client is already installed
   Use the find file feature to see if the file 'SearchLauncher' already exists. If it does, try running it and see if it displays a help message and prompts to quit. If so, then it is most likely already installed.
   
   
3. How to install the batch client
   Install Win32-perl, restart your computer, then download the perl script Win32-search-launcher2.8.pl file as text.
   
   
4. How to run the batch client
   • You must have internet access to run the batch client.
   • Change the Perl path.
     Before you run, change the header of the batch client perl script to your perl path:
     #!/your_perl_path/perl
     
     
   • Start the Search Launcher.
     Open the Windows Explorer, double click the batch client file (for instance, win_sl.pl). The DOS window will start up.
     
     
   • Select the type of your sequence, protein or dna.
     

     Enter type of sequence ([protein seq(s)]/dna seq(s)/output file(s)/seq ID file(s)):

     The default is protein. A list of searches will display:
     

     General protein sequence/pattern searches:
     1  BLASTP+BEAUTY / nr protein - NCBI's Gapped BLASTP with
        BCM's BEAUTY post-processing - NCBI/BCM (beauty_nr)
     2  BLASTP+BEAUTY / nr protein - NCBI's BLASTP
        with BCM's BEAUTY post-processing - NCBI/BCM (beauty_nr_un)
     3  WU-BLASTP+BEAUTY / nr protein - WU-BLAST 2.0 with gapped alignments &
        BEAUTY post-processing - WU/BCM (blast2p_b)
     	       

   • Select the search:

     Enter number or name of search (? for help):

     There are two ways to run the searches:
     • Type in the search number you want to run. For example, 1 for BLASTP+BEAUTY / nr protein.
     • Another way is to use the program name which is at the end of of each searches. For example, beauty_nr for BLASTP+BEAUTY / nr protein search.
     
     
   • Input your sequence file(s):

     Enter file name (wildcard okay, return when done):
     	       

     You can have multiple inputs. For each correct input files, the batch client will tell you the files that have been selected. Hit enter twice after the last sequence input.
     
     
   • Submit search
     After entering all your sequence files and hitting enter, you searches will be submit to the Search Launcher web server automatically. You will see a message:
     

     	       Submitting searches as background task, check the file search-launcher.log
     	       

     View the file search-launcher.log to see if there were any any problems with the search. The final results will be stored in the directory where you run the search-launcher command.

1. System Requirements
   Perl version 5 or higher. If not, then you will have to install perl first. Installing perl will require some time and disk space. Consider asking your system manager or other knowledgeable person for advice. Check our downloads page for a link to the latest version.
   
   -AppleScript (included in MacOS 7.5 and above).
   -MacTCP (included in MacOS 7.5 and above).
   
   

   How to check if the batch client is already installed
   Use the find file feature to see if the file 'SearchLauncher' already exists. If it does, try running it and see if it displays a help message and prompts to quit. If so, then it is most likely already installed.
   
   

   Installing the batch client
   Two installation methods are possible.
   

   • Download the runtime and install it. The runtime includes enough of the perl installation to run without perl separately installed. There have been problems with this type of installation when the file is retrieved using a Browser (Netscape) instead of an ftp program (Fetch). Use Fetch to retrieve the mac-search-launcher-2.6.run.hqx or mac-sl-2.6.run.pl.bin file. If you have mac-search-launcher-2.6.run.hqx, double click. It will generate a program mac-search-launcher-2.6.run.
   • Install MacPerl, then download the perl script search-launcher-2.6.pl file as text and open it using MacPerl. Save the MacPerl file as a droplet under the name Search-Launcher or as a runtime. Run it by dropping a sequence file on it to make sure it is working, it will display a help message and prompt to quit.

   
   

   How to run the batch client

   • You must have internet access to run the batch client.
   • Start the Search Launcher.
     Get your sequence file(s) ready, drop your sequence file(s) onto the icon mac-search-launcher-2.6.run.
     
     
   • Select the type of your sequence, protein or dna.
     

     Enter type of sequence ([protein seq(s)]/dna seq(s)/output file(s)/seq ID file(s)):

     The default is protein. A list of searches will display:
     

     General protein sequence/pattern searches:
     1  BLASTP+BEAUTY / nr protein - NCBI's Gapped BLASTP with
        BCM's BEAUTY post-processing - NCBI/BCM (beauty_nr)
     2  BLASTP+BEAUTY / nr protein - NCBI's BLASTP
        with BCM's BEAUTY post-processing - NCBI/BCM (beauty_nr_un)
     3  WU-BLASTP+BEAUTY / nr protein - WU-BLAST 2.0 with gapped alignments &
        BEAUTY post-processing - WU/BCM (blast2p_b)
     	       

   • Select the search:

     Enter number or name of search (? for help):

     There are two ways to run the searches:
     • Type in the search number you want to run. For example, 1 for BLASTP+BEAUTY / nr protein.
     • Another way is to use the program name which is at the end of of each searches. For example, beauty_nr for BLASTP+BEAUTY / nr protein search.
     
     
   • Input your sequence file(s):

     Enter file name (wildcard okay, return when done):
     	       

     You can have multiple inputs. For each correct input files, the batch client will tell you the files that have been selected. Hit enter when finishing sequence inputs.
     
     
   • Submit search
     After entering all your sequence files and hitting enter, you searches will be submit to the Search Launcher web server automatically. You will see a message:
     

     	       Submitting searches as background task, check the file search-launcher.log
     	       

     The final results will be stored in the directory where the search-launcher batch client resides.

1. Sequence file format
   The Search Launcher Batch Client has been designed to retrieve the sequence in FASTA and /or GENEBANK format using the GI number and Accession number. All the GI and the Accession numbers can be stored in a file. For instance, a sequence file with GI numbers:

         3705822
         3414285
         41604
         

   and a sequence file with Accession numbers:

         AI10079
         AT000751
         X03239
         

2. How to run the Batch Client
   • Start the Search Launcher
     Please refers the help to run the Batch Client at different platform, Unix, Windows 95/98/NT, and Mac.
   • Select the type of your sequence.
     

     Enter type of sequence ([protein seq(s)]/dna seq(s)/output file(s)/seq ID file(s)):

     Enter seq here. A list of searches will display:
     

     Retrieve FASTA Formatted Sequences:
       1  Using file of NCBI-gi identifier(s) - NCBI/BCM (fgi_get)
       2  Using file of accession number identifier(s) - NCBI/BCM (fac_get)
     
     Retrieve GENBANK Formatted Sequences:
       3  Using file of NCBI-gi identifier(s) - NCBI/BCM (ggi_get)
       4  Using file of NCBI-gi identifier(s) with text output (ggit_get)
       5  Using file of accession number identifier(s) - NCBI/BCM (gac_get)
       6  Using file of accession number identifer(s) with text output (gact_get)
     	    

   • Select the search:

     Enter number or name of search (? for help):

     There are two ways to run the searches:
     • Type in the search number you want to run. For example, 1 for Using file of NCBI-gi identifier(s).
     • Another way is to use the program name which is at the end of of each searches. For example, fgi_get for Using file of NCBI-gi identifier(s) search.
     
     
   • Input your sequence file(s):

     Enter file name (wildcard okay, return when done):
     	    

     You can have multiple inputs. For each correct input files, the batch client will tell you the files that have been selected. Hit enter twice after the last sequence input.
     
     
   • Submit search
     After entering all your sequence files and hitting enter, you searches will be submit to the Search Launcher web server automatically. You will see a message:
     

     	    Submitting searches as background task, check the file search-launcher.log
     	    

     The final results will be stored in the directory where you run the search-launcher command.

1. To download the Search Launcher Batch Client software via web, please use Internet Explorer instead of Netscape. We also recommend use FTP softwares, such as Fetch for Mac, and WS_FTP for Windows platform.
2. Download the Batch Client