Description:
The Staden molecular sequence analysis software. (Moderated)
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Error codes
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Hello !!! Please I would like to know about the meaning of some pregap4's error codes. In file pregap.log the information about the failed files (here just two) is: home/... /10f.exp (EXP) ERROR: screen_vector: 11r.exp (???) ERROR: gap4_assemble: failed with code 1 basically I use the same setup with many files and just few has error... more »
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How to install Staden 1.7.0 on Mac OS 10.5?
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Hi, I have a stupid question. I'm trying to install Staden 1.7.0 on Mac OS 10.5. After I unzip the file that I downloaded from Softpedia ([link] Download-27956.html), I can't figure out how to install it. Can anyone tell me tell me how to do it? Thanks!... more »
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gap4 running problem load_alignment_matrix error
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Hi, I am trying to install Staden Gap4 on a 64 bit machine with Ubuntu installed. It appears that trev & pregap will start. But when I type gap4& I get this message - invalid command name "load_alignment_matrix" while executing "load_alignment_matrix [keylget gap_defs ALIGNMENT.MATRIX_FILE]"... more »
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phred and pregap4
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Hello, I apologise in advance if this is a stupid question. I couldn't seem to find this in the staden help documentation. Where do I install phred so that it can be accessed by the pregap4 phred module. Thank you, Glenn
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invalid command name "open_db"
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Hello, staden-linux-1-6-0 here. It seems that 'open_db' is missing from this release?! I tried "find $STADENROOT -name open_db" to no avail ... (and yes, $STADENROOT is set correctly). I was going through $STADENROOT/course/ unix_docs/course_unix.pdf, and I got as far as page 30 (36), when gap4 failed with the error:... more »
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permission for publication
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Dear Staden developers, I would like to know if I need any special permission from you you to publish a screenshot created by your software Trev (trace viewer)? If yes, please let me know what should I do to get it. Thank you, Alla L.Lapidus, Ph.D DOE_JGI
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UNIX Trev (trace viewer) now freely available
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Dear Staden developers, I am contacting you to find out whether I need to get a special permission from you to publish screen shots generated by using Trev (in addition to the reference)? Thank you, Alla
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Staden installation issues
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Hi, I am unable to get staden to work. I essentially wish to use gap4. I downloaded the linux-bin and got stash error when trying gap4. I had already set the STADENROOT variable and sourced the staden.profile file. [m049157@crick5 staden-linux-1-5-3]$ ./linux-bin/gap4 ./linux-bin/gap4: line 123: exec: stash: not found... more »
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gap4 running problem load_alignment_matrix gap.tcl
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Hi I have installed staden on one of my 64 bit machines with Centos5. After some pain, it runs beautifully. Attempting installation on a second machine (actually just copying the appropriate dierctory containing the staden packege to the new machine) which is (supposed to be) similar to the first one I get.... more »
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Fwd: Error during installing Staden-src-1-7-0 package
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Hallo Jean, .. I solved the problem you had using the following procedure: The problem is indeed the compiled libz.a . To recompile that piece using the -fPIC compiler option solves the problem. How to do this: 1. go into the directory <wherever_you_inst_it>/src/zli b (zlib should be a symlink to zlib-1.2.2)... more »
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