Once Vacceed is started, each resource listed after the “name”
key is consecutively executed. Resource names can be in any order
or even excluded with the exception of VALIDATE (see Note 2)
and EVIDENCE (see Note 3), which must always be the first and
last in the list, respectively. Any key in the configuration file can be
used as a variable replacement in the rest of the configuration file.
That is, a “$” character preceding a word denotes a variable; for
example, $work_dir is replaced by “$HOME/vacceed” throughout the configuration file on execution.
Typical Vacceed run times are dependent on various factors
including numbers of proteins to process, programs to execute
(resources), computer processors (cores), and the amount of memory. For example, a test with 500 proteins processed through all
resources completed in 3 h, 21 min, and 17 s using Red Hat
Enterprise Linux Workstation release 7.5, 64 bit kernel, and
32 MB memory with 8 cores; however, the same test without the
resources MHCI and MHCII completed in 23 min and 54 s.
Vacceed takes advantage of multicore processors. By default, the
proteins to process are split into subsets by the number of cores and
then each subset is processed in parallel.
3 Methods
3.1 Running Vacceed
with Sample Data
The Vacceed installation provides sample data comprising a small
collection of Toxoplasma gondii proteins as input. The purpose of
this section is to test the Vacceed installation.
1. Install Vacceed (see Note 4).
2. Edit the species configuration file “toxoplasma.ini” located in
the directory/vacceed/start/config_dir (where
is the directory in which Vacceed was installed).
Under the [Resources] header, remove MHCI and MHCII (see
Note 5).
3. Under the [Main] header, change the current path assigned to
work_dir to install_dir/vacceed/.
4. Under the [Main] header, assign an appropriate e-mail address
to email_url.
5. In a command-line terminal, change directory to install_dir/
vacceed/start.
6. Enter the command: perl startup tg.
7. An e-mail is automatically sent either when the pipeline is
successfully completed or immediately when an error occurs.
A log file is attached to the e-mail providing details of success or
failure (see Note 6).
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Stephen J. Goodswen et al.
key is consecutively executed. Resource names can be in any order
or even excluded with the exception of VALIDATE (see Note 2)
and EVIDENCE (see Note 3), which must always be the first and
last in the list, respectively. Any key in the configuration file can be
used as a variable replacement in the rest of the configuration file.
That is, a “$” character preceding a word denotes a variable; for
example, $work_dir is replaced by “$HOME/vacceed” throughout the configuration file on execution.
Typical Vacceed run times are dependent on various factors
including numbers of proteins to process, programs to execute
(resources), computer processors (cores), and the amount of memory. For example, a test with 500 proteins processed through all
resources completed in 3 h, 21 min, and 17 s using Red Hat
Enterprise Linux Workstation release 7.5, 64 bit kernel, and
32 MB memory with 8 cores; however, the same test without the
resources MHCI and MHCII completed in 23 min and 54 s.
Vacceed takes advantage of multicore processors. By default, the
proteins to process are split into subsets by the number of cores and
then each subset is processed in parallel.
3 Methods
3.1 Running Vacceed
with Sample Data
The Vacceed installation provides sample data comprising a small
collection of Toxoplasma gondii proteins as input. The purpose of
this section is to test the Vacceed installation.
1. Install Vacceed (see Note 4).
2. Edit the species configuration file “toxoplasma.ini” located in
the directory
Under the [Resources] header, remove MHCI and MHCII (see
Note 5).
3. Under the [Main] header, change the current path assigned to
work_dir to install_dir/vacceed/.
4. Under the [Main] header, assign an appropriate e-mail address
to email_url.
5. In a command-line terminal, change directory to install_dir/
vacceed/start.
6. Enter the command: perl startup tg.
7. An e-mail is automatically sent either when the pipeline is
successfully completed or immediately when an error occurs.
A log file is attached to the e-mail providing details of success or
failure (see Note 6).
32
Stephen J. Goodswen et al.