How to add dccp patches to ns2 2.34? Please give me detailed steps.
The file is the file is ns234-dccp-1.patch.
The error comes when I try to simulate dccp is
Kar#ubuntu:~$ ns audiodccp.tcl
invalid command name "Agent/DCCP/TCPlike"
while executing
"Agent/DCCP/TCPlike create _o726 "
invoked from within
"catch "$className create $o $args" msg"
invoked from within
"if [catch "$className create $o $args" msg] {
if [string match "__FAILED_SHADOW_OBJECT_" $msg] {
delete $o
return ""
}
global errorInfo
error "class $..."
(procedure "new" line 3)
invoked from within
"new Agent/DCCP/TCPlike"
invoked from within
"set dccp1 [new Agent/DCCP/TCPlike]"
(file "audiodccp.tcl" line 50)
UBUNTU-10.04
NS2 allinone 2.34
audiodccp.tcl : Unknown file.
invalid command name "Agent/DCCP/TCPlike"
→ → You have a failed build. Or you are using the wrong executable 'ns'. The suggestion is to do :
cd ns-allinone-2.34/-ns-2.34/
cp ns ns-dccp
sudo cp ns-dccp /usr/local/bin/
... and then do simulations with $ ns-dccp [file.tcl]
You can also use ns-2.35, which has DCCP included by default.
Note : You can have as many times ns-allinone-2.xx as you want, installed at the same time. But : Do never add any PATH text to .bashrc. Not required.
Related
i'm new to nf-core/nextflow and needless to say the documentation does not reflect what might be actually implemented. But i'm defining the basic pipeline below:
nextflow.enable.dsl=2
process RUNBLAST{
input:
val thr
path query
path db
path output
output:
path output
script:
"""
blastn -query ${query} -db ${db} -out ${output} -num_threads ${thr}
"""
}
workflow{
//println "I want to BLAST $params.query to $params.dbDir/$params.dbName using $params.threads CPUs and output it to $params.outdir"
RUNBLAST(params.threads,params.query,params.dbDir, params.output)
}
Then i'm executing the pipeline with
nextflow run main.nf --query test2.fa --dbDir blast/blastDB
Then i get the following error:
N E X T F L O W ~ version 22.10.6
Launching `main.nf` [dreamy_hugle] DSL2 - revision: c388cf8f31
Error executing process > 'RUNBLAST'
Error executing process > 'RUNBLAST'
Caused by:
Not a valid path value: 'test2.fa'
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
I know test2.fa exists in the current directory:
(nfcore) MN:nf-core-basicblast jraygozagaray$ ls
CHANGELOG.md conf other.nf
CITATIONS.md docs pyproject.toml
CODE_OF_CONDUCT.md lib subworkflows
LICENSE main.nf test.fa
README.md modules test2.fa
assets modules.json work
bin nextflow.config workflows
blast nextflow_schema.json
I also tried with "file" instead of path but that is deprecated and raises other kind of errors.
It'll be helpful to know how to fix this to get myself started with the pipeline building process.
Shouldn't nextflow copy the file to the execution path?
Thanks
You get the above error because params.query is not actually a path value. It's probably just a simple String or GString. The solution is to instead supply a file object, for example:
workflow {
query = file(params.query)
BLAST( query, ... )
}
Note that a value channel is implicitly created by a process when it is invoked with a simple value, like the above file object. If you need to be able to BLAST multiple query files, you'll instead need a queue channel, which can be created using the fromPath factory method, for example:
params.query = "${baseDir}/data/*.fa"
params.db = "${baseDir}/blastdb/nt"
params.outdir = './results'
db_name = file(params.db).name
db_path = file(params.db).parent
process BLAST {
publishDir(
path: "{params.outdir}/blast",
mode: 'copy',
)
input:
tuple val(query_id), path(query)
path db
output:
tuple val(query_id), path("${query_id}.out")
"""
blastn \\
-num_threads ${task.cpus} \\
-query "${query}" \\
-db "${db}/${db_name}" \\
-out "${query_id}.out"
"""
}
workflow{
Channel
.fromPath( params.query )
.map { file -> tuple(file.baseName, file) }
.set { query_ch }
BLAST( query_ch, db_path )
}
Note that the usual way to specify the number of threads/cpus is using cpus directive, which can be configured using a process selector in your nextflow.config. For example:
process {
withName: BLAST {
cpus = 4
}
}
Let's pretend I'm running something like this:
jq -nr --arg target /tmp \
'(["echo","Hello, world"]|#sh)+">\($target)/sample.txt"' \
| sh
Everything is fine unless I forgot to pass variable $target:
$ jq -nr '(["echo","Hello, world"]|#sh)+">\($target)/sample.txt"'
jq: error: $target is not defined at <top-level>, line 1:
(["echo","Hello, world"]|#sh)+">\($target)/sample.txt"
jq: 1 compile error
How can I catch this and use default value?
I've tried:
$target?
($target)?
try $target catch null
$target? // null
But it seems to be parsing-time error, which obviously can't be caught at runtime. Have I've missed any dynamic syntax?
I've found that command-line arguments can be found in $ARGS.name, but there are two drawbacks:
This was introduced in version 1.6, but I have 1.5 on CentOS 7.
It doesn't catch locally defined variables.
Assuming you need to do something more useful with jq than write 'Hello World' over a text file. I propose the following,
Maybe we can learn some programming tips from Jesus:
"Give to Caesar what belongs to Caesar, and give to God what belongs to God"
Suppose that Caesar is bash shell and God is jq, bash is appropriate to work and test the existence of files, directories and environment variables, jq is appropriate to process information in json format.
#!/bin/bash
dest_folder=$1
#if param1 is not given, then the default is /tmp:
if [ -z $dest_folder ]; then dest_folder=/tmp ; fi
echo destination folder: $dest_folder
#check if destination folder exists
if [ ! -d $dest_folder ]
then
echo "_err_ folder not found"
exit 1
fi
jq -nr --arg target $dest_folder '(["echo","Hello, world"]|#sh)+">\($target)/sample.txt"' | sh
#if the file is succesfully created, return 0, if not return 1
if [ -e "$dest_folder/sample.txt" ]
then
echo "_suc_ file was created ok"
exit 0
else
echo "_err_ when creating file"
exit 1
fi
Now you can include this script as a step in a more complex batch, because it is congruent with linux style, returning 0 on success.
I have a file abc/xyz.log in log directory. How can I find if the file exists or not in SystemVerilog class. If the file exists I want to delete the file.
Thanks.
You can use $fopen and it returns 0 if it doesn't exist. If it does exist, $fclose the file and then use $system("shell command") to delete it.
Using the Unix utility "test" (see "man test") through a $system call can do the job. It can also be done through direct C using the stat() function (much more cumbersome). This example can be leveraged to do what you want. In this case it checks for the existence of a directory and it not found, attempts to create it.
string report_dir;
report_dir = {SIM_ROOT,"/",PROJ_NAME,"/",TECH_PROCESS,"/",LOGNAME,"/doc/functional"};
if ($system($sformatf("/usr/bin/test -d %s", report_dir)) != 0) begin
$display("INFO: creating output directory %s", report_dir);
if($system($sformatf("mkdir -p %s", report_dir)) != 0) begin
$display("ERROR: mkdir -p %s returned an error", report_dir);
$fatal(0);
end
end
if($system($sformatf("/usr/bin/test -d %s -o -w %s", report_dir, report_dir)) != 0) begin
$display("ERROR: output directory %s does not exist or is not writeable", report_dir);
$fatal(0);
end
i too have same problem.
please provide a clear solution for me...
following error is obtained when i run blackhole.tcl file.
ns: _o108 blackhole:
(_o108 cmd line 1)
invoked from within
"_o108 cmd blackhole"
invoked from within
"catch "$self cmd $args" ret"
invoked from within
"if [catch "$self cmd $args" ret] {
set cls [$self info class]
global errorInfo
set savedInfo $errorInfo
error "error when calling class $cls: $args" $..."
(procedure "_o108" line 2)
(SplitObject unknown line 2)
invoked from within
"_o108 blackhole"
Valid examples for the "2005-2013 blackholeaodv code" are : blackholeaodv2005-examples-3-Aug2015.tar.gz
Link : https://drive.google.com/file/d/0B7S255p3kFXNUmJGd0ZyNUhvVFU/view?usp=sharing
I need to edit a .jam file used by boost-build for a specific kind of projects. The official manual on BJAM language says:
One of the toolsets that cares about DEF files is msvc. The following line should be added to it. flags msvc.link DEF_FILE
;
Since the DEF_FILE variable is not used by the msvc.link action, we need to modify it to be: actions link bind DEF_FILE { $(.LD) ....
/DEF:$(DEF_FILE) .... } Note the bind DEF_FILE part. It tells bjam to
translate the internal target name in DEF_FILE to a corresponding
filename in the link
So apparently just printing DEF_FILE with ECHO wouldn't work. How can it be expanded to a string variable or something that can actually be checked?
What I need to do is to print an error message and abort the build in case the flag is not set. I tried:
if ! $(DEF_FILE)
{
errors.user-error "file not found" ;
EXIT ;
}
but this "if" is always true
I also tried putting "if ! $_DEF_FILE {...}" inside the "actions" contained but apparently it is ignored.
I am not sure I understand the global task you have. However, if you wanted to add checking for non-empty DEF_FILE -- expanding on the documentation bit you quote, you need to add the check in msvc.link function.
If you have a command line pattern (specified with 'actions') its content is what is passed to OS for execution. But, you can also have a function with the same name, that will be called before generating the actions. For example, here's what current codebase have:
rule link.dll ( targets + : sources * : properties * )
{
DEPENDS $(<) : [ on $(<) return $(DEF_FILE) ] ;
if <embed-manifest>on in $(properties)
{
msvc.manifest.dll $(targets) : $(sources) : $(properties) ;
}
}
You can modify this code to additionally:
if ! [ on $(<) return $(DEF_FILE) ] {
ECHO "error" ;
}