User: cllezark
cllezark • 20
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- Location:
- Tampa Bay, FL / Hong Kong
- Last seen:
- 3 years, 7 months ago
- Joined:
- 3 years, 7 months ago
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- c*******@eckerd.edu
Posts by cllezark
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Comment:
C: formatting makeblastdb commands
... > The string passed with the -title option is stored somewhere inside the database, it is not the filename of the database.
That's really good to know, piet; thank you for posting. Would I be better off not including the -title option in my command? Also, will I be able the command you submitted ...
written 3.6 years ago by
cllezark • 20
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Comment:
A: formatting makeblastdb commands
... I just got part of the way there with
makeblastdb -in ~/db/nucleotide/Genus_species_DNA_cds.fasta -title GspeciesDNA -dbtype nucl -parse_seqids -out ~/db/nucleotide/GspeciesDNA
The above command put the files where I wanted them, with the name I wanted. But -parse_seqids produced more files ...
written 3.6 years ago by
cllezark • 20
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... I have a couple of .fasta files which I want to turn into databases using the makeblastdb program stored in Blast+ 2.4.0 for OS X 10.11. After following the manual, I typed in this command
makeblastdb -in ~/db/nucleotide/Genus_species_DNA_cds.fasta -title Genus_species_DNA -dbtype nucl - ...
written 3.6 years ago by
cllezark • 20
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... Nailed it. Thanks for the link! ...
written 3.6 years ago by
cllezark • 20
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... I recently installed ncbi-blast-2.4.0+.dmg, but it did not contain the file "ncbi_package_info" that previous versions contained. I had some difficulty setting the path needed to run makeblastdb at first, as it would return the error "command not found" when I attempted to execute the command. After ...
written 3.6 years ago by
cllezark • 20
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... After some creative file rearrangement, I've finally got Viroblast Activated on the server! Thank you so, so much!! For those following at home, move you uncompressed "Viroblast" folder from wherever it is in your system to the `localhost/~User/`directory – that's how the viroblast directory ultimat ...
written 3.6 years ago by
cllezark • 20
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... Apologies for the link, but are these perhaps the files I'm looking for? If they are, I can't find the directory that they make following uncompression.
http://postimg.org/image/4podyse7r/ ...
written 3.6 years ago by
cllezark • 20
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... I have downloaded the source code, for sure. I'm almost certain that the source code is somewhere different from where these commands are being executed. The file is stored in `/Library/WebServer/Documents/viroblast-2.5.3.tar.gz` , which is not nested within `/~User/` (Device-name:~ User$ in the te ...
written 3.6 years ago by
cllezark • 20
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... Not yet solved, but for the first time I got a different response! Trying `tar -zxvf viroblast.tar.gz` returned `tar: Error opening archive: Failed to open 'viroblast.tar.gz'` which isn't yet what I'm looking for, but it's at least different! ...
written 3.6 years ago by
cllezark • 20
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... I am a newcomer to the world of server-usage, database design, php, and SQL; I have used NCBI's BLAST enough to be more than comfortable with it, though. I'm building a database for a few species' worth of sequences, and I need to use ViroBLAST for the built-in search functionality (I have no say in ...
written 3.6 years ago by
cllezark • 20
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