Following the accepted answer to Running phpunit tests using HHVM (HipHop), I attempted to run some tests:
unit-tests/ [develop] > hhvm $(which phpunit) --colors -c phpunit.xml --testsuite all .
/usr/bin/env php -d allow_url_fopen=On -d detect_unicode=Off /usr/local/Cellar/phpunit/4.3.4/libexec/phpunit-4.3.4.phar $*
It appears that this is a command to run the tests (which it does), but I'm confused about
why it's printing this command instead of just running the tests
whether executing that command even uses HHVM, since it starts with /usr/bin/env php...
Does anyone have any insight into this? Thanks so much!
What happened here is that you installed PHPUnit using homebrew, so it created a wrapper script for the actual PHAR file. That wrapper script is a Bash script that runs the PHPUnit PHAR and that script is what you're trying to get HHVM to run. Since it's not a PHP or Hack script, the Bash script is outputted directly.
Instead, you probably want to try to execute $(brew --prefix phpunit)/libexec/phpunit*.phar
e.g.: hhvm $(brew --prefix phpunit)/libexec/phpunit*.phar --colors -c phpunit.xml --testsuite all .
The wildcard is so that you don't need to specify the version of PHPUnit being using.
Related
I am currently having problems using TinyTeX in a conda environment with Snakemake. I have to install TinyTeX installation files using the command tinytex::install_tinytex() before running the pipeline. This installs TinyTeX outside of the created environment (which isn't that big of a problem... but not preferred either) . The main problem is that every time I execute my Snakemake pipeline it will try to reinstall this installation which I don't want. Could anyone tell me what the easiest way is for me to check whether it's installed already? Should I be using the command Rscript -e \"tinytex:::is_tinytex()\" with an if-statement? And what is the best way to write that if-statement by calling Rscript -e in Snakemake? Or should I just write a boolean text-file on first run which specifies whether TinyTeX has been installed before?
It kinda sucks that the TinyTeX conda dependency doesn't work on its own without additional installation...
Snakemake rule (ignore input/output):
rule assembly_report_rmarkdown:
input:
rules.assembly_graph2image_bandage.output,
rules.assembly_assessment_quast.output,
rules.coverage_calculator_shortreads.output,
rules.coverage_calculator_longreads.output
output:
config["outdir"] + "Hybrid_assembly_report.pdf"
conda:
"envs/r-rmarkdown.yaml"
shell:
"""
cp report/RMarkdown/Hybrid_assembly_report.Rmd {config[outdir]}Hybrid_assembly_report.Rmd
Rscript -e \"tinytex::install_tinytex()\"
Rscript -e \"rmarkdown::render('{config[outdir]}Hybrid_assembly_report.Rmd')\"
rm -f {config[outdir]}Hybrid_assembly_report.Rmd {config[outdir]}Hybrid_assembly_report.tex
"""
Conda YAML:
name: r-rmarkdown
channels:
- conda-forge
- bioconda
dependencies:
- r-base=4.0.3
- r-rmarkdown=2.5
- r-tinytex=0.27
Thanks in advance.
I think I've solved the issue. Instead of calling Rscript -e, I have put the following if-statement in the setup chunk in R Markdown (Which runs before running any other code if i'm correct). I then proceeded to uninstall TinyTeX to see whether it will install for once only which it did.
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
if (!tinytex:::is_tinytex()){
tinytex::install_tinytex()
}
I'm new to python and I've been working on a script that will automatically set up development environments. So i have a laundry list of things I need to add to the script and one of them is the latest gradle-5.4.1. I'm running into an issue when I try to add gradle into $PATH on Centos7. After I run this function and run a gradle -v and check the $PATH, it's never concatenated into PATH variable. We need to be able to run gradle from anywhere and I cant seem to figure out how to do this.
def install_gradle():
print("Initiating gradle 5.4.1 install.....")
os.system("sudo wget https://services.gradle.org/distributions/gradle-5.4.1-bin.zip -P /tmp")
os.system("sudo unzip -d /opt/gradle /tmp/gradle-5.4.1-bin.zip")
os.environ("export PATH=$PATH:/opt/gradle/gradle-5.4.1/bin")
I've tried that last line with both os.system and os.environ, neither worked so not sure how to get this to work using python.
Thanks in advance for any input.
So this is what worked for me, editing the bashrc file seemed to resolve the my question:
def install_gradle():
print("Initiating gradle 5.4.1 install.....")
print("Downloading gradle file to tmp directory")
os.system("sudo wget https://services.gradle.org/distributions/gradle-5.4.1-bin.zip -P /tmp")
print("Unzipping gradle installation to /opt/gradle")
os.system("sudo unzip -d /opt/gradle /tmp/gradle-5.4.1-bin.zip")
print("Changing directories to /etc/bashrc")
bashrc_file = open("/etc/bashrc", "a+")
print("Appending PATH environment variables to bashrc file")
bashrc_file.write("export PATH=/opt/gradle/gradle-5.4.1/bin:$PATH")
bashrc_file.close()
I installed Go with homebrew and it usually works. Following the tutorial here on creating serverless api in Go. When I try to run the unit tests, I get the following error:
# _/Users/pro/Documents/Code/Go/ServerLess
main_test.go:6:2: cannot find package "github.com/strechr/testify/assert" in any of:
/usr/local/Cellar/go/1.9.2/libexec/src/github.com/strechr/testify/assert (from $GOROOT)
/Users/pro/go/src/github.com/strechr/testify/assert (from $GOPATH)
FAIL _/Users/pro/Documents/Code/Go/ServerLess [setup failed]
Pros-MBP:ServerLess Santi$ echo $GOROOT
I have installed the test library with : go get github.com/stretchr/testify
I would appreciate it if anyone could point me in the right direction.
Also confusing is when I run echo $GOPATH it doesnt return anything. same goes for echo $GOROOT
Some things to try/verify:
As JimB notes, starting with Go 1.8 the GOPATH env var is now optional and has default values: https://rakyll.org/default-gopath/
While you don't need to set it, the directory does need to have the Go workspace structure: https://golang.org/doc/code.html#Workspaces
Once that is created, create your source file in something like: $GOPATH/src/github.com/DataKid/sample/main.go
cd into that directory, and re-run the go get commands:
go get -u -v github.com/stretchr/testify
go get -u -v github.com/aws/aws-lambda-go/lambda
Then try running the test command again: go test -v
The -v option is for verbose output, the -u option ensures you download the latest package versions (https://golang.org/cmd/go/#hdr-Download_and_install_packages_and_dependencies).
Building BioPerl
Reading skip patterns from 'INSTALL.SKIP'.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/usr/local/bin'
Do not have write permissions on '/usr/local/bin'
6. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
I cannot install bioperl on my linux,It happened when I run command 11 below:
7. git clone https://github.com/bioperl/bioperl-live.git
8. cd bioperl-live
9. perl Build.PL
10. ./Build test
11. ./Build install
Do not have write permissions on '/usr/local/bin'
Looks like you need to run the build script as root, so use the 'sudo' command like
sudo ./Build install
On a separate note, is there a specific reason you need to compile Bioperl from source? Using your distro's package manager would be the easiest way to go about getting bioperl running with the least number of headaches. Check out https://bioperl.org/INSTALL.html for a number of options for installing.
I'm running Jenkins on a Linux host. I'm automating the build of a C++ application. In order to build the application I need to use the 4.7 version of g++ which includes support for c++11. In order to use this version of g++ I run the following command at a command prompt:
exec /usr/bin/scl enable devtoolset-1.1 bash
So I created a "Execute shell" build step and put the following commands, which properly builds the C++ application on the command prompt:
exec /usr/bin/scl enable devtoolset-1.1 bash
libtoolize
autoreconf --force --install
./configure --prefix=/home/tomcat/.jenkins/workspace/project
make
make install
cd procs
./makem.sh /home/tomcat/.jenkins/workspace/project
The problem is that Jenkins will not run any of the commands after the "exec /usr/bin/scl enable devtoolset-1.1 bash" command, but instead just runs the "exec" command, terminates and marks the build as successful.
Any ideas on how I can re-structure the above so that Jenkins will run all the commands?
Thanks!
At the begining of your "Execute shell" script, execute source /opt/rh/devtoolset-1.1/enable to enable the devtoolet "inside" of your shell.
Which gives:
source /opt/rh/devtoolset-1.1/enable
libtoolize
autoreconf --force --install
./configure --prefix=/home/tomcat/.jenkins/workspace/project
make
make install
cd procs
./makem.sh /home/tomcat/.jenkins/workspace/project
I needed to look up what scl actually does.
Examples
scl enable example 'less --version'
runs command 'less --version' in the environment with collection 'example' enabled
scl enable foo bar bash
runs bash instance with foo and bar Software Collections enabled
So what you are doing is running a bash shell. I guess, that the bash shell returns immediately, since you are in non-interactive mode. exec runs the the command within the shell without creating a new shell. That means if the newly opened bash ends it also ends your shell prematurely. I would suggest to put all your build steps into a bash script (e.g. run_my_build.sh) and call it in the following way.
exec /usr/bin/scl enable devtoolset-1.1 run_my_build.sh
This kind of thing normally works in "find" commands, but may work here. Rather than running two, or three processes, you run one "sh" that executes multiple things, like this:
exec sh -c "thing1; thing2; thing3"
If you require each step to succeed before the next step, replace the semi-colons with double ampersands:
exec sh -c "thing1 && thing2 && thing3"
I have no idea which of your steps you wish to run together, so I am hoping you can adapt the concept to fit your needs.
Or you can put the whole lot into a script and exec that.