I've tried variations of this, but had no luck other than the ability to start a cygwin window. (wrapped on ; for clarity)
Filename: "c:\cygwin\bin\bash.exe";
Parameters: "-c c:/scripts/step1.sh paramX";
Flags: shellexec waituntilterminated;
StatusMsg: "Running the script..."
(this is for an internal install, thus cywin is installed, and all paths, scripts are known)
Your problem is that -c tells bash to read instructions from the next parameter:
e.g.
c:\cygwin\bin\bash.exe -c 'for NUM in 1 2 3 4 5 6 7 8 9 10; do echo $NUM; done'
you just need:
c:\cygwin\bin\bash.exe "/scripts/step1.sh paramX"
So your code would look like:
Filename: "c:\cygwin\bin\bash.exe";
Parameters: "c:/scripts/step1.sh paramX";
Flags: shellexec waituntilterminated;
StatusMsg: "Running the script..."
Maybe this will be helpful for somebody else :)
I think you're going to need to make the whole thing part of a cmd.exe invocation, and then I'm not sure it will do exactly what you want/need.
I'm looking at Inno-Setup 5 documentation (may be out-of-date), but I don't think you need the shellexec or waituntilterminated flags.
Try something like
Filename: "cmd.exe"; Parameters: "/c c:\cygwin\bin\bash -c 'c:/scripts/step1.sh paramx'"
Untested, caveat emptor.
Related
There is a small project which produces a binary application. The source code is C, I'm using autotools to create the Makefile and build the binary - it works as well.
I would like to run tests cases with that binary. Here is what I did:
SUBDIRS = src
dist_doc_DATA = README
TESTS=
TESTS+=tests/config1.conf
TESTS+=tests/config2.conf
TESTS+=tests/config3.conf
TESTS+=tests/config4.conf
TESTS+=tests/config5.conf
TESTS+=tests/config6.conf
TESTS+=tests/config7.conf
TESTS+=tests/config8.conf
TESTS+=tests/config9.conf
TESTS+=tests/config10.conf
TESTS+=tests/config11.conf
I would like to run these cases as argument with the tool. When I run make check, I got:
make[3]: Entering directory '/home/airween/src/mytool'
FAIL: tests/config1.conf
FAIL: tests/config2.conf
FAIL: tests/config3.conf
which is correct, because those files are simple configurations files.
How can I solve that make check runs my tool with the scripts above, and finally I get a list with number of success, failed, ... tests, like in that case:
============================================================================
Testsuite summary for mytool 0.1
============================================================================
# TOTAL: 11
# PASS: 0
# SKIP: 0
# XFAIL: 0
# FAIL: 11
# XPASS: 0
# ERROR: 0
Edit: so I would like to emulate these runs:
for f in `ls -1 tests/*.conf; do src/mytool ${f}; done
but - of course - I want to see the summary at the end.
Thanks.
The Autotools' built-in test runner expects you to specify the names of executable tests via the make variable TESTS. You cannot just put random filenames in there and expect make or Automake to know what to do with them.
The tests can be built programs, generated scripts, static scripts distributed with the project, or any combination of the above.
How can I solve that make check runs my tool with the scripts above, and finally I get a [test summary report]?
You have acknowledged that your configuration files are not scripts, so stop calling them that! This is in fact the crux of the problem. The easiest solution is probably to create actual executable scripts, one for each case, and name those in your TESTS variable. Each one would run the binary under test with the appropriate configuration file (that is, you're responsible for making them do that if those are the tests you want to perform).
See also the Automake Manual's chapter on tests.
Okay, the solution from here:
tests/Makefile.am:
==================
TEST_EXTENSIONS = .conf
CONF_LOG_COMPILER = ./test-suit.sh
TESTS=
TESTS+=config1.conf
TESTS+=config2.conf
TESTS+=config3.conf
TESTS+=config4.conf
TESTS+=config5.conf
TESTS+=config6.conf
TESTS+=config7.conf
TESTS+=config8.conf
TESTS+=config9.conf
TESTS+=config10.conf
TESTS+=config11.conf
test/test-suit.sh:
==================
#!/bin/sh
CONF=$1
exec ../src/mytool $CONF
And the result:
make check
...
PASS: config1.conf
PASS: config2.conf
PASS: config3.conf
PASS: config4.conf
PASS: config5.conf
PASS: config6.conf
PASS: config7.conf
PASS: config8.conf
PASS: config9.conf
PASS: config10.conf
PASS: config11.conf
============================================================================
Testsuite summary for mytool 0.1
============================================================================
# TOTAL: 11
# PASS: 11
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
This is what I expected.
How do I get KDiff3 to automatically do a 3-way merge such that it shows no UI? Ideally, if it succeeds, it returns success, and if it can't (it needs manual merging), it returns an error code.
Everything I've read seems to imply that the following should work:
"c:\Program Files\KDiff3\kdiff3.exe" --auto base.txt src.txt tar.txt -o merge.txt
However, it doesn't. When I run it, a message box pops up that says:
Total number of conflicts: 3
Nr of automatically solved conflicts: 3
Nr of unsolved conflicts: 0
How do I get it to run without this popup, and no GUI at all if it fails?
I figured it out. I need to add a "--cs" and "ShowInfoDialogs=0" to the command line. So this:
"c:\Program Files\KDiff3\kdiff3.exe" --auto base.txt src.txt tar.txt -o merge.txt
...becomes this:
"c:\Program Files\KDiff3\kdiff3.exe" --auto base.txt src.txt tar.txt -o merge.txt --cs "ShowInfoDialogs=0"
...and now it works.
When using tools like picard or fgbio through snakemake wrappers, I keep running into out-of-memory issues. At the moment I resort to direct shell calls, which allow me to set the VMs memory. I would prefer to pass these parameters to the wrapped tools. Is there a way, maybe through the resources directive, passing something like mem_mb=10000? I tried, but have not gotten it to work yet.
I have never used the wrapper directive but looking for example at markduplicates/wrapper.py the shell command is picard MarkDuplicates {snakemake.params} .... So maybe using the params slot works?
rule markdups:
input:
'in.bam',
output:
bam= 'out.bam',
metrics= 'metrics.tmp',
params:
mem= "-Xmx4g",
wrapper:
"0.31.0/bio/picard/markduplicates"
picard should understand that -Xmx... is a java parameter.
According to wrapper sources (https://bitbucket.org/snakemake/snakemake-wrappers/src/bd3178f4b82b1856370bb48c8bdbb1932ace6a19/bio/picard/markduplicates/wrapper.py?at=master&fileviewer=file-view-default), it uses cmdline:
from snakemake.shell import shell
shell("picard MarkDuplicates {snakemake.params} INPUT={snakemake.input} "
"OUTPUT={snakemake.output.bam} METRICS_FILE={snakemake.output.metrics} "
"&> {snakemake.log}")
So you could pass any options using params: "smth" section.
If you check picard excecutable script sources:
cat `which picard`
You will find:
...
pass_args=""
for arg in "$#"; do
case $arg in
'-D'*)
jvm_prop_opts="$jvm_prop_opts $arg"
;;
'-XX'*)
jvm_prop_opts="$jvm_prop_opts $arg"
;;
'-Xm'*)
jvm_mem_opts="$jvm_mem_opts $arg"
;;
*)
if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates'
then
pass_args="$arg"
else
pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg
fi
;;
esac
done
...
So I assume this should work:
rule markdups:
input:
"in.bam",
output:
bam = "out.bam",
metrics = "metrics.tmp",
params:
"-Xmx10000m"
wrapper:
"0.31.0/bio/picard/markduplicates"
I'm trying to test the continuation facility in Pharo, with this code(in the playground):
| cont f |
f:=[
|i|
i:=0.
Continuation currentDo: [ :cc | cont:=cc ].
i:=i+1.
].
f value. "1"
cont. "a Continuation"
However, as soon as I call the continuation saved in cont(replacing cont. by cont value.), the image freezes immediately, and I have to press atl+. to gain back control.
VM version: VM: NBCoInterpreter NativeBoost-CogPlugin-GuillermoPolito.19 uuid: acc98e51-2fba-4841-a965-2975997bba66 May 15 2014 NBCogit NativeBoost-CogPlugin-GuillermoPolito.19 uuid: acc98e51-2fba-4841-a965-2975997bba66 May 15 2014 https://github.com/pharo-project/pharo-vm.git Commit: ed4a4f59208968a21d82fd2406f75c2c4de558b2 Date: 2014-05-15 18:23:04 +0200 By: Esteban Lorenzano <estebanlm#gmail.com> Jenkins build #14826
Pharo version: [version] 4.0 #40614
Thanks.
Edit: I was stupid, didn't think this through...
You've effectively created an infinite loop by reevaluating the same code again and again. You can see that if you debug the code and step through it. The original context will always be restored and then evaluated starting with the first expression following the #currentDo: send. This is exactly what the continuation is supposed to do: save the current position in the execution and restart there later on.
I do not have a Fedora to test, however I tried your code in Ubuntu, using this version of Pharo:
wget -O- get.pharo.org/40+vm | bash
./pharo-ui Pharo.image
and your code seems to work properly :(
In case this error persists, could you be more specific about the version of the vm you are using?:
./pharo Pharo.image --version
And the version of Pharo you are using?:
./pharo Pharo.image printVersion
Also, send us the crash.dmp file would help a lot.
Im having an issue writing a DCL in OpenVMS in that I need the DCL to call a command and capture its output (but not output the output to the screen) Later on in the DCL I then need to print that output I stored.
Heres an example:
ICE SET FASTER !This command sets my environment to the "Faster" environment.
The above command outputs this if executed directly in OpenVMS:
Initialising TEST Environment to FASTER
--------------------------------------------------------------------------------
Using Test Search rules FASTER
Using Test Search rules FASTER
--------------------------------------------------------------------------------
dcl>
So I created a DCL in an attempt to wrap this output in order to display a more simplified output. Heres my code so far:
!************************************************************************
$ !* Wrapper for setting ICE account. Outputs Environment
$ !************************************************************************
$ on error then goto ABORT_PROCESS
$ICE_DCL_MAIN:
$ ice set 'P1'
$ ICE SHOW
$ EXIT
$ABORT_PROCESS:
$ say "Error ICING to: " + P1
$ EXIT 2
[End of file]
In the lines above ICE SET 'P1' is setting the ice environment, but I dont want this output to be echoed to VMS. But what I do want is to write the output of $ICE SHOW into a variable and then echo that out later on in the DCL (most of which ive omitted for simplification purposes)
So what should be outputted should be:
current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]
Instead of:
Initialising TEST Environment to FASTER
--------------------------------------------------------------------------------
Using Test Search rules FASTER
Using Test Search rules FASTER
--------------------------------------------------------------------------------
current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]
Ive had a look through the manual and im getting a bit confused so I figured I tried here. Id appreciate any pointers. Thanks.
EDIT
Here is what ive come up with after the comments, the problem im having is when I connect to VMS using an emulator such as SecureCRT the correct output is echoed. But when I run the DCL via my SSH2 library in .NET it doesnt output anything. I guess thats because it closes the SYS$OUTPUT stream temporarily or something?
$ !************************************************************************
$ !* Wrapper for setting ICE account. Outputs Environment
$ !************************************************************************
$ on error then goto ABORT_PROCESS
$ICE_DCL_MAIN:
$ DEFINE SYS$OUTPUT NL:
$ ice set 'P1'
$ DEASSIGN SYS$OUTPUT
$ ice show
$ EXIT
$ABORT_PROCESS:
$ say "Error ICING to: " + P1
$ EXIT 2
[End of file]
EDIT 2
So I guess really I need to clarify what im trying to do here. Blocking the output doesnt so matter so much, im merely trying to capture it into a Symbol for example.
So in C# for example you can have a method that returns a string. So you'd have string myResult = vms.ICETo("FASTER"); and it would return that and store it in the variable.
I guess im looking for a similar thing in VMS so that once ive iced to the environment I can call:
$ environment == $ICE SHOW
But I of course get errors with that statement
The command $ assign/user_mode Thing Sys$Output will cause output to be redirected to Thing until you $ deassign/user_mode Sys$Output or next executable image exits. An assignment without the /USER_MODE qualifier will persist until deassigned.
Thing can be a logical name, a file specification (LOG.TXT) or the null device (NLA0:) if you simply want to flush the output.
When a command procedure is executed the output can be redirected using an /OUTPUT qualifier, e.g. $ #FOO/output=LOG.TXT.
And then there is piping ... .
You can redirect the output to a temp file and then print its content later:
$ pipe write sys$output "hi" > tmp.tmp
$ ty tmp.tmp
VMS is not Unix, DCL is not Bash: you can not easily set a DCL symbol from the output of a command.
Your ICE SHOW prints one line, correct? The first word is always "current", correct?
So you can create a hack.
First let me fake your ICE command:
$ create ice.com
$ write sys$output "current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]"
^Z
$
and I define a dcl$path pointing to the directory where this command procedure is
so that I can use/fake the command ICE
$ define dcl$path sys$disk[]
$ ice show
current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]
$
Now what you need, create a command procedure which sets a job logical
$ cre deflog.com
$ def/job/nolog mylog "current''p1'"
^Z
$
And I define a command "current" to run that command procedure:
$ current="#deflog """
Yes, you need three of the double quotes at the end of the line!
And finally:
$ pipe (ice show | #sys$pipe) && mysym="''f$log("mylog")'"
$ sh symb mysym
MYSYM = "current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]"
$
On the other hand, I don't know what you are referring to C# and Java. Can you elaborate on that and tell us what runs where?
You can try using: DEFINE /USER SYS$OUTPUT NL:.
It works only for the next command and you dont need to deassign.
Sharing some of my experience here. I used below methods to redirect outputs to files.
Define/Assign the user output and then execute the required command/script afterwards. Output will be written to .
$define /user sys$output <file_path>
execute your command/script
OR
assign /user <file_path> sys$output
execute your command/script
deassign sys$output
To re-direct in to null device like in Unix (mentioned in above answers), you can use 'nl:' instead of
define /user sys$output nl:
or
assign /user nl: sys$output