I am trying to figure out how to set the max-hops against a federated policy that I want to make, but the documentation doesn't say where to put this within the command.
https://www.rabbitmq.com/federated-exchanges.html
Is it just like this, note I have put max-hops at the end:
rabbitmqctl set_policy ha-fed "^MyExchange" '{"federation-upstream-set":"all", "ha-sync-mode":"automatic"' --priority 10 --apply-to exchanges --max-hops 1
or does the max-hops go inside the JSON block?
The documentation doesn't help by saying max-hops=1 which is neither a JSON colon declaration or a command line one with the space?
Any help would be greatly appreciated, many thanks
I believe I have found the answer I was getting confused that it should be in the above command but imagine it belongs in this command around declaring a federated upstream.
Not entirely sure where to specify it in the command, but I did find that the default value is 1 which is just what I wanted anyway.
rabbitmqctl set_parameter federation-upstream upstream-from-cluster2 '{"uri":"amqp://name:password#myipaddress:5674"}'
Related
I'm tinkering with this project where Step 6 requires me to run a command like make db-prepare-artix7. This command corresponds to this section of the Makefile. I am confused by the #+SKIP_ENV=true in the recipe. What is #+SKIP_ENV here, and what does it do? Couldn't find anywhere referring to SKIP_ENV.
Thanks!
Explaining every part:
The # means the command will not be echoed by Make during recipe execution
The + means the command will be executed even during dry runs: make --dry-run ...
The SKIP_ENV=true is sh(ell) syntax for setting the environment variable SKIP_ENV to the string true for the duration of the command that follows
In your case the source ... command
The effect of SKIP_ENV depends on the command - dig deeper to find out
I have the question about the proper handling of the config file. I'm trying to solve my issue for a couple of days now but with the best will, I just can't find out how to do it. I know that this question is maybe quite similar with all the others here and I really tried to use them - but I didn't really get it. I hope that some things about how snakemake works will be more clear when I solved this problem.
I'm just switching to snakemake and I thought I just can easily convert my bash script. To get familiar with snakemake I started trying a simple Data-Processing pipeline. I know I could solve my case while defining every variable within the snakefile. But I want to use an external config file.
First is to say, for better understanding I decided just to post the code which I thought would work somehow. I already played around with different versions for a "rule all" and the "lambda" functions, but nothing worked so far and it just would be confusing. I'm really a bit embarrassed and confused about why I can't get this working. The variable differs from the key because I aways had a version where I redefine the variable, like:
$ sample=config["samples"]
I would be incredibly thankful for an example code.
What I'd like to have is:
The config file:
samples:
- SRX1232390
- SRX2312380
names:
- SomeData
- SomeControl
adapters:
- GATCGTAGC
- GATCAGTCG
And then I thought I can just call the keys like different variables.
rule download_fastq:
output:
"fastq/{name}.fastq.gz"
shell:
"fastq-dump {wildcards.sample} > {output}"
later there will be more rules, so I thought for them I also just need a key:
rule trimming_cutadapt:
input:
"fastq/{name}.fastq"
output:
"ctadpt_{name}.fastq"
shell:
"cutadapt -a {adapt}"
I also tried something with a config file like this:
samples:
Somedata: SRX1232131
SomeControl: SRX12323
But in the end I also didn't find the final solution nor would I know how to add a third "variable" then.
I hope it is somehow understandable what I want to have. It would be very awesome if someone could help me.
EDIT:
Ok - I reworked my code and tried to dig into everything. I fear my understanding lacks in connecting the things I read in this case. I would really appreciate some tips which will probably help me to understand my confusion.
First of all: Rather than try to download data from a pipeline I decided to do this in a config step. I tried out two different versions now:
Based on this answer I tried version one. I like the version with the two files. But I'm stuck in how to deal with the variables now in things like using them with the lambda function or everything where you normally would write "config["sample"]".
So my problem here is that I don't knwo ho to proceed or how the correct syntax is now to call the variables.
#version one
configfile: "config.yaml"
sample_file = config["sample_file"]
import pandas as pd
sample = pd.read_table(sample_file)['samples']
adapt = pd.read_table(sample_file)['adapters']
rule trimming_cutadapt:
input:
data=expand("../data/{sample}.fastq", name = pd.read_table(sample_file)['names']),
lambda wildcards: ???
output:
"trimmed/ctadpt_{sample}.fastq"
shell:
"cutadapt -a {adapt}"
So I went back to try to understand using and defining the wildcards. So (among other things) I looked into the example snakefile and the example rules of Johannes. And of course into the man. Oh and the Thing about the zip function.
At least I don't get an error anymore that it can't deal with wildcards or whatever. Now it's just doing nothing. And I can't find out why because I don't get any information. Additionaly I marked some points which I don't understand.
#version two
configfile: "config_ChIP_Seq_Pipeline.yaml"
rule all:
input:
expand("../data/{sample}.fastq", sample=config["samples"])
#when to write the lambda or the expand in a rule all and when into the actual rule?
rule trimming_cutadapt:
input:
"../data/{sample}.fastq"
params:
adapt=lambda wildcards: config[wildcards.sample]["adapt"] #why do I have to write .samle? when I have to use wildcard.XXX in the shell part?
output:
"trimmed/ctadpt_{sample}.fastq"
shell:
"cutadapt -a {params.adapt}"
As a testfile I used this one.
My configfile in version 1:
sample_file: "sample.tab"
and the tab file:
samples names adapters
test_1 input GACCTA
and the configfile from version two:
samples:
- test_1
adapt:
- GTACGTAG
Thanks for your help and patients!
Cheers
You can look at this post to see how to store and access sample information.
Then you can look at Snakemake documentation here, more specifically at the zip function, which might help you as well.
Based on steps in http://scip.zib.de/doc/html/TEST.php, I have managed to set up an automated test using SCIP. However, I'd like to write the solution (best feasible solution) to a file, instead of just getting the objective value. Is there anyway to do it in the automated test?
I did a hack in check.sh by replacing
OPTCOMMAND=optimize; write solution myfilename.sol;
But too bad, it doesn't seem to work, when I tried to make TEST=mytest test, this line is observed from the output
bash ./check.sh mytest bin/scip-3.1.0.linux.x86_64.gnu.opt.spx default scip-3.1.0.linux.x86_64.gnu.opt.spx 3600 2100000000 6144 1 default 10000 false false 3.1.0 spx false /tmp optimize;
write: solution is not logged in on myfilename.sol
I know it is possible to write the solution via interactive shell, but I am trying to automate the test in order to retrieve both solution and obj value. Any help or clarification will be much appreciated!
You are getting an error because with the syntax you are using, you try to invoke a bash command called "write" because of the semicolon:
The write utility allows you to communicate with other users, by
copying lines from your terminal to theirs.
Just try without semicolon ;)
The cleaner solution would be to modify the file "check/configuration_tmpfile_setup_scip.sh"
and add the line
echo write solution /absolute/path/to/solutions/${INSTANCE}.sol >> $TMPFILE
before the quit command. This configuration file sets up a batch file to feed SCIP with all commands that the interactive shell should execute, and you can model arbitrary user behavior.
I am using HCatalog's WebHCat API to run Pig jobs, such as documented here:
https://cwiki.apache.org/confluence/display/Hive/WebHCat+Reference+Pig
I have no problem running a simple job but I would like to attach a parameters file to the job, such as one can do using pig command line's parameter: --param_file .
I assume this is possible through arg request's parameter, so I tried multiple things, such as passing:
'arg': '-param_file /path/to/param.file'
or:
'arg': {'param_file': '/path/to/param.file'}
None seems to work, and error stacks don't say much.
I would love to know if this is possible, and if so, how to correctly achieve this.
Many thanks
Correct usage:
'arg': ['-param_file', '/path/to/param.file']
Explanation:
By passing the value in arg,
'arg': {'-param_file': '/path/to/param.file'}
webhcat generates "-param_file" for the command prompt.
Pig throws the following error
ERROR org.apache.pig.Main - ERROR 2999: Unexpected internal error. Can not create a Path from a null string
Using a comma instead of the colon operator passes the path to file as a second argument.
webhcat will generate "-param_file" "/path/to/param.file"
P.S: I am using Requests library on python to make the REST calls
I have a variable
android="/media/New Volume_/android-sdk-linux_86"
I get an error saying that it cannot find the directory
I changed it to android="/media/New\ Volume_/android-sdk-linux_86"
I still get the same error. I even tried
android="/media/'New Volume_'/android-sdk-linux_86"
and I am using "$android" everywhere ...
I am not able to find the error, can someone help me..
Thanks
Take it this is bash? You assign variables with spaces like this:
android="/media/New Volume_/android-sdk-linux_86"
(Note you don't use the $ notation when setting a value.)
And reference them like this:
cd "$android"