I have the basic "input can be single end or paired end reads" problem for my snakemake pipeline. I'd like to use unpack if possible, since it seems designed for this situation (as illustrated in the answer for this issue), but I also want to use conda:, which requires shell:. I believe that shell: will die if I have {input.read2} but it's not provided by unpack(). Is there any good way of getting around this besides either 1) creating 2 nearly identical rules 2) making an empty read2 (if single-end) and then creating an if-else in shell to check for whether read2 is empty. Neither is ideal.
Try to combine your input function with a params function to generate the flags for either paired or single end. Using the bowtie example from your link:
def bowtie2_inputs(wildcards):
if (seq_type == "pe"):
return expand("{reads}_{strand}.fastq", strand=["R1", "R2"], reads=wildcards.reads)
elif (seq_type == "se"):
return expand("{reads}.fastq", reads=wildcards.reads)
def bowtie2_params(wildcards, input):
if (seq_type == "pe"):
return f'-1 {input.reads[0]} -2 {input.reads[1]}'
else:
return f'-U {input.reads}'
rule bowtie2:
input:
reads=bowtie2_inputs,
index=bowtie2_index
output:
sam="{reads}_bowtie2.sam"
params:
file_args=bowtie2_params
conda: <env>
shell:
"bowtie2 -x {input.index} {params.file_args} -S {output.sam}"
Not sure it's any better than the shell option. I would use two rules with a ruleorder preferring the paired ends. That would be easier to modify if you wanted say a different aligner or to change parameters for each case. As is this requires a bit of jumping around to actually see what the rule does.
I am currently working on making a CICD script to deploy a complex environment into another environment. We have multiple technology involved and I currently want to optimize this script because it's taking too much time to fetch information on each environment.
In the OpenShift 3.6 section, I need to get the last successful deployment for each application for a specific project. I try to find a quick way to do so, but right now I only found this solution :
oc rollout history dc -n <Project_name>
This will give me the following output
deploymentconfigs "<Application_name>"
REVISION STATUS CAUSE
1 Complete config change
2 Complete config change
3 Failed manual change
4 Running config change
deploymentconfigs "<Application_name2>"
REVISION STATUS CAUSE
18 Complete config change
19 Complete config change
20 Complete manual change
21 Failed config change
....
I then take this output and parse each line to know which is the latest revision that have the status "Complete".
In the above example, I would get this list :
<Application_name> : 2
<Application_name2> : 20
Then for each application and each revision I do :
oc rollout history dc/<Application_name> -n <Project_name> --revision=<Latest_Revision>
In the above example the Latest_Revision for Application_name is 2 which is the latest complete revision not building and not failed.
This will give me the output with the information I need which is the version of the ear and the version of the configuration that was used in the creation of the image use for this successful deployment.
But since I have multiple application, this process can take up to 2 minutes per environment.
Would anybody have a better way of fetching the information I required?
Unless I am mistaken, it looks like there are no "one liner" with the possibility to get the information on the currently running and accessible application.
Thanks
Assuming that the currently active deployment is the latest successful one, you may try the following:
oc get dc -a --no-headers | awk '{print "oc rollout history dc "$1" --revision="$2}' | . /dev/stdin
It gets a list of deployments, feeds it to awk to extract the name $1 and revision $2, then compiles your command to extract the details, finally sends it to standard input to execute. It may be frowned upon for not using xargs or the like, but I found it easier for debugging (just drop the last part and see the commands printed out).
UPDATE:
On second thoughts, you might actually like this one better:
oc get dc -a -o jsonpath='{range .items[*]}{.metadata.name}{"\n\t"}{.spec.template.spec.containers[0].env}{"\n\t"}{.spec.template.spec.containers[0].image}{"\n-------\n"}{end}'
The example output:
daily-checks
[map[name:SQL_QUERIES_DIR value:daily-checks/]]
docker-registry.default.svc:5000/ptrk-testing/daily-checks#sha256:b299434622b5f9e9958ae753b7211f1928318e57848e992bbf33a6e9ee0f6d94
-------
jboss-webserver31-tomcat
registry.access.redhat.com/jboss-webserver-3/webserver31-tomcat7-openshift#sha256:b5fac47d43939b82ce1e7ef864a7c2ee79db7920df5764b631f2783c4b73f044
-------
jtask
172.30.31.183:5000/ptrk-testing/app-txeq:build
-------
lifebicycle
docker-registry.default.svc:5000/ptrk-testing/lifebicycle#sha256:a93cfaf9efd9b806b0d4d3f0c087b369a9963ea05404c2c7445cc01f07344a35
You get the idea, with expressions like .spec.template.spec.containers[0].env you can reach for specific variables, labels, etc. Unfortunately the jsonpath output is not available with oc rollout history.
UPDATE 2:
You could also use post-deployment hooks to collect the data, if you can set up a listener for the hooks. Hopefully the information you need is inherited by the PODs. More info here: https://docs.openshift.com/container-platform/3.10/dev_guide/deployments/deployment_strategies.html#lifecycle-hooks
Someone can tell if it is possible, save a variable(a number (this number is a total of rows in a SQL tabel)) in like a memory or a file? and then, like 5 min later, check if the number is the same? and send me like a warning or alert for nagios?
Sounds like you are looking to do something like this:
#!/bin/sh
OLD_NUM=`command_to_get_number`
while true
do
sleep 5m
NEW_NUM=`command_to_get_number`
[ "$OLD_NUM" != "$NEW_NUM" ] && notify-send "Number changed"
OLD_NUM="$NEW_NUM"
done
notify-send will give you a desktop notification, not sure if there is a similar command to work with nagios.
Suppose I have 2 test suites in the local directory, foo and bar, and I want to run the test suite in the order of foo then bar.
I tried to run pybot -s foo -s bar ., but then it just goes and run bar then foo (i.e. in alphabetical order).
Is there a way to get pybot to run robot framework suites to be execute in the order that I define?
Robot framework can use argument files that can be used to specify order of execution (docs):
This is from older docs (not online anymore):
Another important usage for argument files is specifying input files or directories in certain order. This can be very useful if the alphabetical default execution order is not suitable:
Basically, you create something similar to start up script.
--name My Example Tests
tests/some_tests.html
tests/second.html
tests/more/tests.html
tests/more/another.html
tests/even_more_tests.html
There is neat feature that from argument file you can call another argument file that can override previously set parameters. Execution is recursive, so you can nest as many argument files as you need
Another option would be to use start up script. Than you have to deal with other aspects like which operating system you are running test on. You could also use python for starting up script on multiple platforms. There is more in this section of docs
If there are multiple test case files in an RF directory , the execution order can be specified by giving numbers as prefixes to test case names , like this.
01__my_suite.html -> My Suite
02__another_suite.html -> Another Suite
Such prefixes are not included in the generated test suite name if they are separated from the base name of the suite with two underscores:
More details are here.
http://robotframework.org/robotframework/latest/RobotFrameworkUserGuide.html#execution-order
You can use tagging.
Tag the tests as foo and bar so you can run each test separately:
pybot -i foo tests
or
pybot -i bar tests
and decide the order
pybot -i bar tests || pybot -i foo tests
or in a script.
The drawback is that you have to run the setup for each test.
Would something like this be of any use?
pybot tests/test1.txt tests/test2.txt
So, to reverse:
pybot tests/test2.txt tests/test1.txt
I had success using a listener:
Listener.py:
class Listener(object):
ROBOT_LISTENER_API_VERSION = 3
def __init__(self):
self.priorities = ['foo', 'bar']
def start_suite(self, data, suite):
#data.suites is a list of <TestSuite> instances
data.suites = self.rearrange(data.suites)
def rearrange(self, suites=[]):
#Do some sorting of suites based on self.priorities e.g. using bubblesort
n = len(suites)
if n > 1:
for i in range(0, n):
for j in range(0, n-i-1):
#Initialize the compared suites with lowest priority
priorityA = 0
priorityB = 0
#If suite[j] is prioritized, get the priority of it
if str(suites[j]) in self.priorities:
priorityA = len(self.priorities)-self.priorities.index(str(suites[j]))
#If suite[j+1] is prioritized, get the priority of it
if str(suites[j+1]) in self.priorities:
priorityB = len(self.priorities)-self.priorities.index(str(suites[j+1]))
#Compare and swap if suite[j] is of lower priority than suite[j+1]
if priorityA < priorityB:
suites[j], suites[j+1] = suites[j+1], suites[j]
return arr
Assuming foo.robot and bar.robot are contained in a toplevel suite called 'tests', you can run it like this:
pybot --listener Listener.py tests/
This will rearrange childsuites on the fly. It's possible you can modify it upfront using a prerunmodifier instead.
It's the first great virtue of programmers. All of us have, at one time or another automated a task with a bit of throw-away code. Sometimes it takes a couple seconds tapping out a one-liner, sometimes we spend an exorbitant amount of time automating away a two-second task and then never use it again.
What tiny hack have you found useful enough to reuse? To make go so far as to make an alias for?
Note: before answering, please check to make sure it's not already on favourite command-line tricks using BASH or perl/ruby one-liner questions.
i found this on dotfiles.org just today. it's very simple, but clever. i felt stupid for not having thought of it myself.
###
### Handy Extract Program
###
extract () {
if [ -f $1 ] ; then
case $1 in
*.tar.bz2) tar xvjf $1 ;;
*.tar.gz) tar xvzf $1 ;;
*.bz2) bunzip2 $1 ;;
*.rar) unrar x $1 ;;
*.gz) gunzip $1 ;;
*.tar) tar xvf $1 ;;
*.tbz2) tar xvjf $1 ;;
*.tgz) tar xvzf $1 ;;
*.zip) unzip $1 ;;
*.Z) uncompress $1 ;;
*.7z) 7z x $1 ;;
*) echo "'$1' cannot be extracted via >extract<" ;;
esac
else
echo "'$1' is not a valid file"
fi
}
Here's a filter that puts commas in the middle of any large numbers in standard input.
$ cat ~/bin/comma
#!/usr/bin/perl -p
s/(\d{4,})/commify($1)/ge;
sub commify {
local $_ = shift;
1 while s/^([ -+]?\d+)(\d{3})/$1,$2/;
return $_;
}
I usually wind up using it for long output lists of big numbers, and I tire of counting decimal places. Now instead of seeing
-rw-r--r-- 1 alester alester 2244487404 Oct 6 15:38 listdetail.sql
I can run that as ls -l | comma and see
-rw-r--r-- 1 alester alester 2,244,487,404 Oct 6 15:38 listdetail.sql
This script saved my career!
Quite a few years ago, i was working remotely on a client database. I updated a shipment to change its status. But I forgot the where clause.
I'll never forget the feeling in the pit of my stomach when I saw (6834 rows affected). I basically spent the entire night going through event logs and figuring out the proper status on all those shipments. Crap!
So I wrote a script (originally in awk) that would start a transaction for any updates, and check the rows affected before committing. This prevented any surprises.
So now I never do updates from command line without going through a script like this. Here it is (now in Python):
import sys
import subprocess as sp
pgm = "isql"
if len(sys.argv) == 1:
print "Usage: \nsql sql-string [rows-affected]"
sys.exit()
sql_str = sys.argv[1].upper()
max_rows_affected = 3
if len(sys.argv) > 2:
max_rows_affected = int(sys.argv[2])
if sql_str.startswith("UPDATE"):
sql_str = "BEGIN TRANSACTION\\n" + sql_str
p1 = sp.Popen([pgm, sql_str],stdout=sp.PIPE,
shell=True)
(stdout, stderr) = p1.communicate()
print stdout
# example -> (33 rows affected)
affected = stdout.splitlines()[-1]
affected = affected.split()[0].lstrip('(')
num_affected = int(affected)
if num_affected > max_rows_affected:
print "WARNING! ", num_affected,"rows were affected, rolling back..."
sql_str = "ROLLBACK TRANSACTION"
ret_code = sp.call([pgm, sql_str], shell=True)
else:
sql_str = "COMMIT TRANSACTION"
ret_code = sp.call([pgm, sql_str], shell=True)
else:
ret_code = sp.call([pgm, sql_str], shell=True)
I use this script under assorted linuxes to check whether a directory copy between machines (or to CD/DVD) worked or whether copying (e.g. ext3 utf8 filenames -> fusebl
k) has mangled special characters in the filenames.
#!/bin/bash
## dsum Do checksums recursively over a directory.
## Typical usage: dsum <directory> > outfile
export LC_ALL=C # Optional - use sort order across different locales
if [ $# != 1 ]; then echo "Usage: ${0/*\//} <directory>" 1>&2; exit; fi
cd $1 1>&2 || exit
#findargs=-follow # Uncomment to follow symbolic links
find . $findargs -type f | sort | xargs -d'\n' cksum
Sorry, don't have the exact code handy, but I coded a regular expression for searching source code in VS.Net that allowed me to search anything not in comments. It came in very useful in a particular project I was working on, where people insisted that commenting out code was good practice, in case you wanted to go back and see what the code used to do.
I have two ruby scripts that I modify regularly to download all of various webcomics. Extremely handy! Note: They require wget, so probably linux. Note2: read these before you try them, they need a little bit of modification for each site.
Date based downloader:
#!/usr/bin/ruby -w
Day = 60 * 60 * 24
Fromat = "hjlsdahjsd/comics/st%Y%m%d.gif"
t = Time.local(2005, 2, 5)
MWF = [1,3,5]
until t == Time.local(2007, 7, 9)
if MWF.include? t.wday
`wget #{t.strftime(Fromat)}`
sleep 3
end
t += Day
end
Or you can use the number based one:
#!/usr/bin/ruby -w
Fromat = "http://fdsafdsa/comics/%08d.gif"
1.upto(986) do |i|
`wget #{sprintf(Fromat, i)}`
sleep 1
end
Instead of having to repeatedly open files in SQL Query Analyser and run them, I found the syntax needed to make a batch file, and could then run 100 at once. Oh the sweet sweet joy! I've used this ever since.
isqlw -S servername -d dbname -E -i F:\blah\whatever.sql -o F:\results.txt
This goes back to my COBOL days but I had two generic COBOL programs, one batch and one online (mainframe folks will know what these are). They were shells of a program that could take any set of parameters and/or files and be run, batch or executed in an IMS test region. I had them set up so that depending on the parameters I could access files, databases(DB2 or IMS DB) and or just manipulate working storage or whatever.
It was great because I could test that date function without guessing or test why there was truncation or why there was a database ABEND. The programs grew in size as time went on to include all sorts of tests and become a staple of the development group. Everyone knew where the code resided and included them in their unit testing as well. Those programs got so large (most of the code were commented out tests) and it was all contributed by people through the years. They saved so much time and settled so many disagreements!
I coded a Perl script to map dependencies, without going into an endless loop, For a legacy C program I inherited .... that also had a diamond dependency problem.
I wrote small program that e-mailed me when I received e-mails from friends, on an rarely used e-mail account.
I wrote another small program that sent me text messages if my home IP changes.
To name a few.
Years ago I built a suite of applications on a custom web application platform in PERL.
One cool feature was to convert SQL query strings into human readable sentences that described what the results were.
The code was relatively short but the end effect was nice.
I've got a little app that you run and it dumps a GUID into the clipboard. You can run it /noui or not. With UI, its a single button that drops a new GUID every time you click it. Without it drops a new one and then exits.
I mostly use it from within VS. I have it as an external app and mapped to a shortcut. I'm writing an app that relies heavily on xaml and guids, so I always find I need to paste a new guid into xaml...
Any time I write a clever list comprehension or use of map/reduce in python. There was one like this:
if reduce(lambda x, c: locks[x] and c, locknames, True):
print "Sub-threads terminated!"
The reason I remember that is that I came up with it myself, then saw the exact same code on somebody else's website. Now-adays it'd probably be done like:
if all(map(lambda z: locks[z], locknames)):
print "ya trik"
I've got 20 or 30 of these things lying around because once I coded up the framework for my standard console app in windows I can pretty much drop in any logic I want, so I got a lot of these little things that solve specific problems.
I guess the ones I'm using a lot right now is a console app that takes stdin and colorizes the output based on xml profiles that match regular expressions to colors. I use it for watching my log files from builds. The other one is a command line launcher so I don't pollute my PATH env var and it would exceed the limit on some systems anyway, namely win2k.
I'm constantly connecting to various linux servers from my own desktop throughout my workday, so I created a few aliases that will launch an xterm on those machines and set the title, background color, and other tweaks:
alias x="xterm" # local
alias xd="ssh -Xf me#development_host xterm -bg aliceblue -ls -sb -bc -geometry 100x30 -title Development"
alias xp="ssh -Xf me#production_host xterm -bg thistle1 ..."
I have a bunch of servers I frequently connect to, as well, but they're all on my local network. This Ruby script prints out the command to create aliases for any machine with ssh open:
#!/usr/bin/env ruby
require 'rubygems'
require 'dnssd'
handle = DNSSD.browse('_ssh._tcp') do |reply|
print "alias #{reply.name}='ssh #{reply.name}.#{reply.domain}';"
end
sleep 1
handle.stop
Use it like this in your .bash_profile:
eval `ruby ~/.alias_shares`