NCBI submission: Difference between revisions
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1. makeConinfo ASSEMBLY.coninfo | 1. makeConinfo ASSEMBLY.coninfo | ||
2. buildAssemblyArchive ASSEMBLY.coninfo --prompt --subname umd-20070816-125223 | 2. buildAssemblyArchive ASSEMBLY.coninfo --prompt --subname umd-20070816-125223 | ||
problems: | |||
conformation: always LINEAR | |||
taxid: not recognized | |||
3. validate: | 3. validate: | ||
oXygen: software used by NCBI; license required | oXygen: software used by NCBI; license required | ||
xmllint: open source | xmllint: open source | ||
$ xmllint --schema ASSEMBLY.xsd ASSEMBLY.xml > /dev/null | $ xmllint --schema ASSEMBLY.xsd ASSEMBLY.xml > /dev/null | ||
Revision as of 18:09, 17 August 2007
NCBI
seqin: standalone application
Compressed archive containing 2 files: ASSEMBLY.xml , MD5 Accepted only by uploading to NCBI FTP server. server: ftp-private.ncbi.nlm.nih.gov login: umd_trc passwd: center: UMD description: University of Maryland ASSEMBLY XML Schema png ASSEMBLY XML Schema xsd
Procedure
Files:
.contig, .seq, .qual, .seq_name2ti
Steps:
1. makeConinfo ASSEMBLY.coninfo
2. buildAssemblyArchive ASSEMBLY.coninfo --prompt --subname umd-20070816-125223
problems:
conformation: always LINEAR
taxid: not recognized
3. validate:
oXygen: software used by NCBI; license required
xmllint: open source
$ xmllint --schema ASSEMBLY.xsd ASSEMBLY.xml > /dev/null