I'm executing multiple libraries from user.r.
I can get the path of the script from system/script/path but I can't see how I can get the name of the script. So am I obliged to hardcode the file name in header property like below (File):
REBOL [
Title: "Lib1"
File: "lib1.r"
]
script-path: ""
]
system/script/header/script-path: rejoin [system/script/path system/script/header/file]
probe system/script/header/script-path
input
system/options/script does only give the full script name and path of the first script passed by dos command line (not if it is executed in console) and not the path of subsequent scripts called by the very first one.
What I want is the full path of the subsequents scripts.
So it seems there's no solution!
Try help system/options and you will find the information you are lookimg for.
Related
I have an error when i run nextflow consist of the following sentence
Error executing process > 'BWA_INDEX (Homo_sapiens_assembly38_chr1.fasta)'
Caused by:
Missing output file(s) FASTA.* expected by process 'BWA_INDEX(Homo_sapiens_assembly38_chr1.fasta)'
I use the following script.
#!/usr/bin/env nextflow
params.PublishDir = "/home/nextflow_test/genesFilter"
params.pathFasta = "/home/nf-core/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38_chr1.fasta"
InputFasta = file(params.pathFasta)
process BWA_INDEX {
tag {InputFasta.name}
publishDir (
path: "${params.PublishDir}",
mode: 'copy',
overwrite: 'true',
saveAs: "${params.PublishDir}/${it}"
)
input:
path InputFasta
output:
file("FASTA.*") into bwa_indexes
script:
"""
bwa-mem2 index "${InputFasta}"
"""
}
ch_bwa = bwa_indexes
Nevertheless into the work directory (specified after the error sentence) the process does work correctly and the output files are generated but not on my desire output directory. I tried to replace the "file" by the "path" on the script in the line:
output:
file("FASTA.*")
As well as replace "FASTA.* " for "${params.PublishDir}/FASTA.*"
but the error still appears. I don't know exactly why it happens. ¿Maybe could be due to the use of params to specify the inputs and outputs?
Thanks in advance!
Missing output file(s) FASTA.* expected by process 'BWA_INDEX(Homo_sapiens_assembly38_chr1.fasta)'
Nextflow is expecting files matching the glob pattern FASTA.* in the working directory, but they could not be found when the process exited (successfully). You just need to tell Nextflow what files to expect in your output declaration. The files that bwa-mem2 index Homo_sapiens_assembly38_chr1.fasta should have created might look like:
Homo_sapiens_assembly38_chr1.fasta.0123
Homo_sapiens_assembly38_chr1.fasta.amb
Homo_sapiens_assembly38_chr1.fasta.ann
Homo_sapiens_assembly38_chr1.fasta.bwt.2bit.64
Homo_sapiens_assembly38_chr1.fasta.bwt.8bit.32
Homo_sapiens_assembly38_chr1.fasta.pac
The following output declaration should be sufficient to find these files:
output:
path("${InputFasta}.*") into bwa_indexes
Note that only files that are declared in your output block are published to the publishDir. Also, the 'saveAs' publishDir parameter must be a closure for it to work correctly. You will need to fix this (or just remove the line entirely) to make your example work.
Is it possible to get the full path of the current file within a live template in IntelliJ? I've tried using groovyScript("new File('.').absolutePath") function, but that returns /Applications/IntelliJ IDEA.app/Contents/bin/. and not the file path as I was hoping for.
Thanks!
According to the docs (emphasis mine):
You can use groovyScript macro with multiple arguments. The first argument is a script text that is executed or a path to the file that contains a script. The next arguments are bound to _1, _2, _3, ..._n variables that are available inside your script. Also, _editor variable is available inside the script. This variable is bound to the current editor.
The _editor is an instance of EditorImpl which holds a reference to the VirtualFile that represents the currently opened file.
Therefore, the following script gets the full path of currently opened file.
groovyScript("_editor.getVirtualFile().getPath()")
Or if you want to get the path relative to the project's root:
groovyScript("_editor.getVirtualFile().getPath().replace(_editor.getProject().getBaseDir().getPath(), \"\")")
Since IntelliJ IDEA 2019.3 the Live Template macros filePath() and fileRelativePath() are available. A complicated Groovy script macro is no longer required.
How can I find out (with Windows a batch command), if, for example, a variable starts with ABC?
I know that I can search for variables if I know the whole content (if "%variable%"=="abc"), but I want that it only looks after the beginning.
I also need it to find out where the batch file is located, so if there is a other command that reveals the file's location, please let me know.
Use the variable substring syntax:
IF "%variable:~0,3%"=="ABC" [...]
If you need the path to the batch file without the batch file name, you can use the variable:
%~dp0
Syntax for this is explained in the help for the for command, although this variable syntax extends beyond just the for command syntax.
to find batch file location use %0 (gives full patch to current batch file) or %CD% variable which gives local directory
When developing Pig scripts that use the STORE command I have to delete the output directory for every run or the script stops and offers:
2012-06-19 19:22:49,680 [main] ERROR org.apache.pig.tools.grunt.Grunt - ERROR 6000: Output Location Validation Failed for: 'hdfs://[server]/user/[user]/foo/bar More info to follow:
Output directory hdfs://[server]/user/[user]/foo/bar already exists
So I'm searching for an in-Pig solution to automatically remove the directory, also one that doesn't choke if the directory is non-existent at call time.
In the Pig Latin Reference I found the shell command invoker fs. Unfortunately the Pig script breaks whenever anything produces an error. So I can't use
fs -rmr foo/bar
(i. e. remove recursively) since it breaks if the directory doesn't exist. For a moment I thought I may use
fs -test -e foo/bar
which is a test and shouldn't break or so I thought. However, Pig again interpretes test's return code on a non-existing directory as a failure code and breaks.
There is a JIRA ticket for the Pig project addressing my problem and suggesting an optional parameter OVERWRITE or FORCE_WRITE for the STORE command. Anyway, I'm using Pig 0.8.1 out of necessity and there is no such parameter.
At last I found a solution on grokbase. Since finding the solution took too long I will reproduce it here and add to it.
Suppose you want to store your output using the statement
STORE Relation INTO 'foo/bar';
Then, in order to delete the directory, you can call at the start of the script
rmf foo/bar
No ";" or quotations required since it is a shell command.
I cannot reproduce it now but at some point in time I got an error message (something about missing files) where I can only assume that rmf interfered with map/reduce. So I recommend putting the call before any relation declaration. After SETs, REGISTERs and defaults should be fine.
Example:
SET mapred.fairscheduler.pool 'inhouse';
REGISTER /usr/lib/pig/contrib/piggybank/java/piggybank.jar;
%default name 'foobar'
rmf foo/bar
Rel = LOAD 'something.tsv';
STORE Rel INTO 'foo/bar';
Once you use the fs command, there a lot of ways to do this. For an individual file, I wound up adding this to the beginning of my scripts:
-- Delete file (won't work for output, which will be a directory
-- but will work for a file that gets copied or moved during the
-- the script.)
fs -touchz top_100
rm top_100
For a directory
-- Delete dir
fs -rm -r out
I'm working on a script that processes a folder and there is always one file in it I need to rename. The new name should be the parent directory name. How do I get this in a batch file? The full path to the dir is known.
It is not very clear how the script is supposed to become acquainted with the path in question, but the following example should at least give you an idea of how to proceed:
FOR %%D IN ("%CD%") DO SET "DirName=%%~nxD"
ECHO %DirName%
This script gets the path from the CD variable and extracts the name only from it to DirName.
You can use basename command:
FULLPATH=/the/full/path/is/known
JUSTTHENAME=$(basename "$FULLPATH")
You can use built-in bash tricks:
FULLPATH=/the/full/path/is/known
JUSTTHENAME=${FULLPATH##*/}
Explanations:
first # means 'remove the pattern from the begining'
second # means 'remove the longer possible pattern'
*/ is the pattern
Using built-in bash avoid to call an external command (i.e. basename) therefore this optimises you script. However the script is less portable.