Description:
The Staden molecular sequence analysis software. (Moderated)
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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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Staden startup
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Hi everyone, Though I tried hard to look at possible solution in the group, I am not able to find (or understand) out an answer. I downloaded staden1.7. I ran makefile.thirdparty It stopped in middle due to error (iwidgets). So I manually installed as written in the Readme document. I copied : export STADENROOT=/usr/local/staden... more »
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error while loading shared libraries: libtk_utils.so
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Hi All I am not the first to experience this so a solution should be available (although I do not have it) I have 64 bit Centos 5 linux on my dual core AMD machine. 1. I have downloaded staden-linux-x86-1-7-0.tar.gz and unpacked in my / usr/local directory 2. My .bash_profile is as follows ...if [ -f ~/.bashrc ]; then... more »
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Probs with pregap4
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Hi, I'm having the same problem as a few others and I've yet to solve it. Every time I try to enter sequences trace files or embl files from pregap4 to gap4, I get the following error message - Report from 'Enter assembly (into Gap4)' - ERR: Failed to change directory to /Users/koquin/Desktop/Sequence Test/... more »
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Staden & ace / 454?
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Hi Could anyone advise me about their experiences of getting 454 Newbler- assembled data into Staden? As far as I can tell, the only format available is .ace? Also, I notice that trev can now display 454 flowgrams, but the sff file we received contains all the fragments in a single file. Is there a way to split this?... more »
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assembly problem with 6700 seq
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Hi all. I'm not so new with Staden Package (integrated with phred/phrap/repeatmasker), but recently I'm facing assembly problems never found before. At the moment, I'm using Staden v.1. 7 on a FedoraCore3 machine. When trying to assemble about 6700 seqs (.ab1 and .SCF), stored on a new 80GB HD (97% free space), I'm getting... more »
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using emboss programs from spin
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Dear all, I have installed on a linux system (Ubuntu 6.06): Staden-1.7.0 EMBOSS 3.0.0 First, I had to make the iwidgets symbolic link in staden-1.7.0/lib to point to the right place: ln -sf /usr/lib/iwidgets4.0.1 iwidgets I wanted to use the spin interface to run emboss programs. So I run create_emboss_files. Because the tcl script assumes a wrong localization... more »
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installing on linux
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Dear all, I'm trying to install staden package on mandriva distribution. I followed the instructions found on internet (make; make install...) but when I try to start gap4 I obtain always the following error message: "stash: error while loading shared libraries: libtk_utils.so: cannot open shared object file: No such file or directory"... more »
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