Migrating the Mad Thought Blog to a new server (mysql, php)

  1. Dump the database data mysqldump --host=localhost --user=root -p journal >journal.sql
  2. Create the databse on the new machine mysql -u root -p CREATE DATABASE journal;
  3. Import the data into the database mysql -p -h localhost journal < journal.sql
  4. Create the user 'journal' GRANT ALL PRIVILEGES ON *.* TO 'journal'@'localhost' IDENTIFIED BY 'journal' WITH GRANT OPTION;

How to transfer the oligo database from MacVec tor to a web-based blast database

1. Save all sequences in one flatfile format (NOT MacVector format), e.g. genbank format.
2. Copy all sequences to a Linux/UNIX computer and convert them from Mac format to UNIX format: mac2unix *.gb
3. Write all sequence fiule names into one file: ls *.gb > oligo.lst
4. Convert all sequences into one file of concatenated fasta entries using EMBOSS: seqret -sequence @oligo.lst -osformat fasta. Call the output file "mcbl_oligo_db"
5. Put this fasta file into the blast web servers database directory (.../blast/db)