Linux - Revision history

Tpillone at 13:30, 20 February 2019

2019-02-20T13:30:13Z

Tpillone at 13:26, 20 February 2019

2019-02-20T13:26:44Z

Tpillone at 11:57, 27 November 2018

2018-11-27T11:57:52Z

Tpillone at 11:57, 27 November 2018

2018-11-27T11:57:34Z

Tpillone at 11:14, 22 November 2018

2018-11-22T11:14:12Z

Tpillone at 13:15, 19 November 2018

2018-11-19T13:15:43Z

Master student at 20:29, 13 November 2018

2018-11-13T20:29:31Z

Master student at 20:29, 13 November 2018

2018-11-13T20:29:07Z

Master student at 20:21, 13 November 2018

2018-11-13T20:21:06Z

Master student at 20:19, 13 November 2018

2018-11-13T20:19:55Z

@@ Line 103: / Line 103: @@
 *add "Port 3389"
-== Bash error handling - exit code ==
+==Bash error handling - exit code==
 Capture exit code in piped commands<syntaxhighlight lang="bash">
@@ Line 115: / Line 114: @@
 fastaStat.py -f genome_fasta.fasta -l | grep contig_40 || true | sed 's//contig_/'
 </syntaxhighlight><br />

@@ Line 1: / Line 1: @@
-== user/groups ==
+==user/groups==
-=== create group and add users to the group ===
+===create group and add users to the group===
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 sudo groupadd metagenlab
@@ Line 12: / Line 12: @@
 </syntaxhighlight>
-* group file conf
+*group file conf
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 cat /etc/group
 </syntaxhighlight>
-== HDD ==
+==HDD==
-* liste des disques
+*liste des disques
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 lsblk -io KNAME,TYPE,SIZE,MODEL
 </syntaxhighlight>
-== utilisation des diques ==
+==utilisation des diques==
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 df -h
 </syntaxhighlight>
-== Docker ==
+==Docker==
-* ubuntu network access problem
+*ubuntu network access problem
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 sudo mv /etc/resolv.conf{,.bak}
 sudo ln -s /etc/resolv.conf /run/systemd/resolve/resolv.conf
 </syntaxhighlight>
-== Atom setup ==
+==Atom setup==
-* [https://jstaf.github.io/2018/03/25/atom-ide.html atom - ipython - Hydrogen package]
+*[https://jstaf.github.io/2018/03/25/atom-ide.html atom - ipython - Hydrogen package]
-== NextFlow ==
+==NextFlow==
-# http://nextflow-io.github.io/patterns/index.html#_get_process_work_directory
+#http://nextflow-io.github.io/patterns/index.html#_get_process_work_directory
-# https://github.com/sanger-pathogens/companion/blob/master/annot.nf#L658
+#https://github.com/sanger-pathogens/companion/blob/master/annot.nf#L658
-# https://nextflow-io.github.io/nf-hack18/training.html#_basic_language_structures_and_commands
+#https://nextflow-io.github.io/nf-hack18/training.html#_basic_language_structures_and_commands
-=== Relauch killed jobs with increased ressources ===
+===Relauch killed jobs with increased ressources===
-<syntaxhighlight line='line'>
+<syntaxhighlight line="line">
 process foo {
@@ Line 69: / Line 69: @@
 </syntaxhighlight>
-=== split input into chunks ===
+===split input into chunks===
-<syntaxhighlight line='line'>
+<syntaxhighlight line="line">
 channel.buffer(size:3)
 </syntaxhighlight>
-=== group channel output into a single list ===
+===group channel output into a single list===
-<syntaxhighlight line='line'>
+<syntaxhighlight line="line">
 query = Channel.fromPath '*.fa'
 species = Channel.from 'human', 'cow', 'horse'
@@ Line 98: / Line 98: @@
 In the above example a BLAST task is executed for each pair of species and query that are received. When the task completes a new tuple containing the value for species and the file result is sent to the blastOuts channel.
-== make SSH listen to alternative port (eg 3389 rdp) ==
+==make SSH listen to alternative port (eg 3389 rdp)==
-* edit "/etc/ssh/sshd_config"
+*edit "/etc/ssh/sshd_config"
-* add "Port 3389"
+*add "Port 3389"

@@ Line 98: / Line 98: @@
 In the above example a BLAST task is executed for each pair of species and query that are received. When the task completes a new tuple containing the value for species and the file result is sent to the blastOuts channel.
-## make SSH listen to alternative port (eg 3389 rdp) ##
+== make SSH listen to alternative port (eg 3389 rdp) ==
 * edit "/etc/ssh/sshd_config"
 * add "Port 3389"

← Older revision		Revision as of 11:57, 27 November 2018
Line 97:		Line 97:

	In the above example a BLAST task is executed for each pair of species and query that are received. When the task completes a new tuple containing the value for species and the file result is sent to the blastOuts channel.		In the above example a BLAST task is executed for each pair of species and query that are received. When the task completes a new tuple containing the value for species and the file result is sent to the blastOuts channel.
		+
		+	## make SSH listen to alternative port (eg 3389 rdp) ##
		+
		+	* edit "/etc/ssh/sshd_config"
		+	* add "Port 3389"

@@ Line 49: / Line 49: @@
 # http://nextflow-io.github.io/patterns/index.html#_get_process_work_directory
 # https://github.com/sanger-pathogens/companion/blob/master/annot.nf#L658
 === Relauch killed jobs with increased ressources ===

← Older revision		Revision as of 13:15, 19 November 2018
Line 46:		Line 46:

	== NextFlow ==		== NextFlow ==
		+
		+	# http://nextflow-io.github.io/patterns/index.html#_get_process_work_directory
		+	# https://github.com/sanger-pathogens/companion/blob/master/annot.nf#L658

	=== Relauch killed jobs with increased ressources ===		=== Relauch killed jobs with increased ressources ===

← Older revision		Revision as of 20:29, 13 November 2018
Line 91:		Line 91:
	}		}
	</syntaxhighlight>		</syntaxhighlight>
		+
		+	In the above example a BLAST task is executed for each pair of species and query that are received. When the task completes a new tuple containing the value for species and the file result is sent to the blastOuts channel.

← Older revision		Revision as of 20:29, 13 November 2018
Line 67:		Line 67:
	=== split input into chunks ===		=== split input into chunks ===

		+	<syntaxhighlight line='line'>
	channel.buffer(size:3)		channel.buffer(size:3)
		+	</syntaxhighlight>
		+	=== group channel output into a single list ===
		+
		+
		+	<syntaxhighlight line='line'>
		+	query = Channel.fromPath '*.fa'
		+	species = Channel.from 'human', 'cow', 'horse'
		+
		+	process blast {
		+
		+	input:
		+	val species
		+	file query
		+
		+	output:
		+	set val(species), file('result') into blastOuts
		+
		+
		+	"blast -db nr -query $query" > result
		+
		+	}
		+	</syntaxhighlight>

← Older revision		Revision as of 20:21, 13 November 2018
Line 64:		Line 64:
	}		}
	</syntaxhighlight>		</syntaxhighlight>
		+
		+	=== split input into chunks ===
		+
		+	channel.buffer(size:3)

← Older revision		Revision as of 20:19, 13 November 2018
Line 43:		Line 43:

	* [https://jstaf.github.io/2018/03/25/atom-ide.html atom - ipython - Hydrogen package]		* [https://jstaf.github.io/2018/03/25/atom-ide.html atom - ipython - Hydrogen package]
		+
		+
		+	== NextFlow ==
		+
		+	=== Relauch killed jobs with increased ressources ===
		+
		+
		+	<syntaxhighlight line='line'>
		+	process foo {
		+
		+	memory { 2.GB * task.attempt }
		+	time { 1.hour * task.attempt }
		+
		+	errorStrategy { task.exitStatus == 140 ? 'retry' : 'terminate' }
		+	maxRetries 3
		+
		+	script:
		+	<your job here>
		+
		+	}
		+	</syntaxhighlight>