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Trailing spaces
Open

Just with this basic configuration, the Hive is able to run Thread_app in 16 cores.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Line length
Open

With this tutorial, our goal is to give insights on how to set up the Hive to run jobs using Shared Memory Parallelism (threads) and Distributed Memory Parallelism (MPI).
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

*Module* provides configuration files (module-files) for the dynamic modification of the user’s environment.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

The resource description is specific to our LSF environment, so adapt it to yours, but:
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Code block style
Open

        sub param_defaults {
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Ordered list item prefix
Open

4. Regenerate docs/hive_schema.html, docs/scripts and docs/doxygen by running make_docs.pl
Severity: Info
Found in docs/release_checklist.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

Line length
Open

eHive is a system for running computation pipelines on distributed computing resources - clusters, farms or grids.
Severity: Info
Found in README.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

* **SGE**. A meadow that supports Sun Grid Engine (now known as Oracle Grid Engine). Available for download on GitHub at [Ensembl/ensembl-hive-sge](https://github.com/Ensembl/ensembl-hive-sge).
Severity: Info
Found in README.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Multiple consecutive blank lines
Open
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD012 - Multiple consecutive blank lines

Tags: whitespace, blank_lines

Aliases: no-multiple-blanks

This rule is triggered when there are multiple consecutive blank lines in the document:

Some text here


Some more text here

To fix this, delete the offending lines:

Some text here

Some more text here

Note: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.

Line length
Open

Here is an excerpt of Ensembl Compara's [ExaML](https://github.com/Ensembl/ensembl-compara/blob/feature/update_pipeline/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/ExaML.pm) MPI module. Note that LSF needs the MPI command to be run through mpirun.lsf
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

            'cmd' => 'cmd 1 ; cmd  2 ; mpirun.lsf -np 64 -mca btl tcp,self #examl_exe# -examl_parameter_1 value1 -examl_parameter_2 value2',
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Ordered list item prefix
Open

   2. Find "Incoming WebHooks" via the search box and select it
Severity: Info
Found in docs/Slack_howto.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

Lists should be surrounded by blank lines
Open

   3. You should be on a page that gives an introduction about WebHooks and
Severity: Info
Found in docs/Slack_howto.md by markdownlint

MD032 - Lists should be surrounded by blank lines

Tags: bullet, ul, ol, blank_lines

Aliases: blanks-around-lists

This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:

Some text
* Some
* List

1. Some
2. List
Some text

To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):

Some text

* Some
* List

1. Some
2. List

Some text

Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.

Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:

* This is
not okay

* This is
  okay

Lists should be surrounded by blank lines
Open

   4. If you scroll down to "Integration Settings" you can give a description
Severity: Info
Found in docs/Slack_howto.md by markdownlint

MD032 - Lists should be surrounded by blank lines

Tags: bullet, ul, ol, blank_lines

Aliases: blanks-around-lists

This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:

Some text
* Some
* List

1. Some
2. List
Some text

To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):

Some text

* Some
* List

1. Some
2. List

Some text

Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.

Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:

* This is
not okay

* This is
  okay

Lists should be surrounded by blank lines
Open

* `input_id` so that the runnable can dataflow jobs with the same parameters
Severity: Info
Found in wrappers/README.md by markdownlint

MD032 - Lists should be surrounded by blank lines

Tags: bullet, ul, ol, blank_lines

Aliases: blanks-around-lists

This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:

Some text
* Some
* List

1. Some
2. List
Some text

To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):

Some text

* Some
* List

1. Some
2. List

Some text

Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.

Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:

* This is
not okay

* This is
  okay

Lists should be surrounded by blank lines
Open

* C
Severity: Info
Found in wrappers/README.md by markdownlint

MD032 - Lists should be surrounded by blank lines

Tags: bullet, ul, ol, blank_lines

Aliases: blanks-around-lists

This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:

Some text
* Some
* List

1. Some
2. List
Some text

To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):

Some text

* Some
* List

1. Some
2. List

Some text

Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.

Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:

* This is
not okay

* This is
  okay

Lists should be surrounded by blank lines
Open

* how many Workers can simultaneously work on a given Analysis,
Severity: Info
Found in README.md by markdownlint

MD032 - Lists should be surrounded by blank lines

Tags: bullet, ul, ol, blank_lines

Aliases: blanks-around-lists

This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:

Some text
* Some
* List

1. Some
2. List
Some text

To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):

Some text

* Some
* List

1. Some
2. List

Some text

Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.

Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:

* This is
not okay

* This is
  okay

Bare URL used
Open

To subscribe to it please visit (http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users)
Severity: Info
Found in README.md by markdownlint

MD034 - Bare URL used

Tags: links, url

Aliases: no-bare-urls

This rule is triggered whenever a URL is given that isn't surrounded by angle brackets:

For more information, see http://www.example.com/.

To fix this, add angle brackets around the URL:

For more information, see <http:></http:>.

Rationale: Without angle brackets, the URL isn't converted into a link in many markdown parsers.

Note: if you do want a bare URL without it being converted into a link, enclose it in a code block, otherwise in some markdown parsers it will be converted:

`http://www.example.com`

No space after hash on atx style header
Open

####If your compute environment uses [Module ](http://modules.sourceforge.net/)
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD018 - No space after hash on atx style header

Tags: headers, atx, spaces

Aliases: no-missing-space-atx

This rule is triggered when spaces are missing after the hash characters in an atx style header:

#Header 1

##Header 2

To fix this, separate the header text from the hash character by a single space:

# Header 1

## Header 2

Code block style
Open

        {   -logic_name => 'app_multi_core',
Severity: Info
Found in docs/MPI_howto.md by markdownlint
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