mryaninsilico
commented
3 years ago Hi. Did you download the 2.3 version: http://projects.insilico.us.com/SpliceSeq_2.3/SpliceSeq.zip?
Also, could you look in the SpliceSeq directory to see if any file with a .log extension has an error message.
Michael Ryan, PhD
In Silico Solutions
From: Minghao Jiang @.*** Sent: Tuesday, April 13, 2021 3:44 AM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Subscribed Subject: [MD-Anderson-Bioinformatics/SpliceSeq] spliceseq can't connect to mysql (#9)
Hi,
I’d like to use SpliceSeq to quantify splicing events in my RNA-seq data. But SpliceSeq can’t connect to MySQL after configuring it.
Settings are:
DBURL jdbc:mysql://localhost
SGDatabase splicegraph
DBUser mjiang
DBPassword mjiang
I'm sure that I can log in mysql through mysql -u mjiang -p -h localhost and there's a database named splicegraph
$mysql -u mjiang -p -h localhost
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 88
Server version: 8.0.23 MySQL Community Server - GPL
Copyright (c) 2000, 2021, Oracle and/or its affiliates.
Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
mysql> use splicegraph;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
mysql> show tables;
+--------------------------+
| Tables_in_splicegraph |
+--------------------------+
| attribute |
| exon |
| graph |
| graph_ncbi_annotation |
| graph_uniprot_annotation |
| graph_uniprot_map |
| isoform |
| isoform_ex_seq |
| protein_feature_ref |
| splice |
| uniprot_exon_align |
| uniprot_feature_ref |
| uniprot_prot_seq |
| version |
+--------------------------+
14 rows in set (0.00 sec)
mysql>
Could you give me some advice about configuring SpliceSeq or mysql? Thanks in advance.
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mhjiang97
Hi,
I’d like to use SpliceSeq to quantify splicing events in my RNA-seq data. But SpliceSeq can’t connect to MySQL after configuring it.
Settings are:
I'm sure that I can log in mysql through
mysql -u mjiang -p -h localhostand there's a database namedsplicegraphCould you give me some advice about configuring SpliceSeq or mysql? Thanks in advance.