I'm getting this error on my mac osx build.
Primer3/eprimer3 issue:
Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified
From:
http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm#globalTags
PRIMER_THERMODYNAMIC_PARAMETERS_PATH (string; default ./primer3_config)
This tag specifies the path to the directory that contains all the parameter files used by the thermodynamic approach. In Linux, there are two default locations that are tested if this tag is not defined: ./primer3_config/ and /opt/primer3_config/. For Windows, there is only one default location: .\primer3_config\.
I put the primer3_config in my PATH in bin and still cannot solve this issue. I even did:
export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/primer3-2.3.2/src
and
export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/primer3-2.3.2/src/primer3_config
to no avail.
According to the primer3 manual:
1.5. IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH must point to the right location.
This tag specifies the path to the directory that contains all the
parameter files used by the thermodynamic approach. In Linux, there
are two default locations that are tested if this tag is not
defined: ./primer3_config/ and /opt/primer3_config/. For Windows,
there is only one default location: .\primer3_config. If the the
parameter files are not in one these locations, be sure to set
PRIMER_THERMODYNAMIC_PARAMETERS_PATH.
So if you download and compile primer3 form source using the Make command, to get primer3 to run globally you need to copy the executueable, primer3_core, to your path and place the configuration directory, primer3_config in that same directory or at /opt/primer3_config
cd src
sudo cp primer3_core /usr/local/bin # or /usr/bin
sudo cp -r primer3_config /opt/
I has the same issue. I had installed Primer 3 using homebrew-science which was pretty painless. https://github.com/Homebrew/homebrew-science
I did try copying the primer3_config directory into the homebrew primer3 directory, ie:
/usr/local/Cellar/primer3/2.3.4/bin/primer3_config but this also did not work.
In the end I added the PRIMER_THERMODYNAMIC_PARAMETERS_PATH configuration to the primer 3 input file, and this worked. Note that the directory name must have a trailing slash. It is the last entry in the file below which is copied from the example file in the primer3 sources.
SEQUENCE_ID=example
SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
PRIMER_TASK=pick_detection_primers
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-100
P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/usr/local/Cellar/primer3/2.3.4/bin/primer3_config/
=
Then run it like this:
$ primer3_core < example2
Related
I'm trying to setup Facebook Duckling on Windows 10.
When I execute: stack exec duckling-example-exe it produces the following error:
duckling-example-exe.EXE: /etc/zoneinfo/: getDirectoryContents:findFirstFile: does not exist (The system cannot find the path specified.)
I don't understand why I'm getting this error since I followed the recommendation on this GitHub thread which suggests replacing "/usr/share/zoneinfo/" in Duckling/exe/ExampleMain.hs with a link to a folder containing the zoneinfo files. You can see I replaced the path as suggested in the screenshot below:
I also tried adding a double slash as seen below - but it didn't help:
I tried with forward slash instead but this didn't help either:
Moreover, I don't understand where the path: /etc/zoneinfo/ is coming from, if the path is no longer present in ExampleMain.hs? Where is the compiler pulling the path from?
Thanks!
You need to run stack exec duckling-example-exe in the directory where the stack.yaml and project.yaml files of the duckling source code is that you are trying to modify. Otherwise it will use the version of duckling from stackage without your changes.
I downloaded Gurobi and verified that my license is working.
I'm trying to add the Gurobi package to Julia, but it seems that the dll file can't be found, even though my GUROBI_HOME variable is okay.
Here is the output of Pkg.build("Gurobi") :
Found GUROBI_HOME = C:\gurobi902\win64
Does this point to the correct install location?
on Windows, this might be C:\Program Files\gurobi810\win64\
alternatively, on Windows, this might be C:/Program Files/gurobi810/win64/
on OSX, this might be /Library/gurobi810/mac64/
on Unix, this might be /home/my_user/gurobi810/linux64/
Note: this has to be a full path, not a path relative to your current
directory or your home directory.
We're going to look for the Gurobi library in this directory:
C:\gurobi902\win64\bin
That directory has the following files:
C:\gurobi902\win64\bin\grbcluster.exe
C:\gurobi902\win64\bin\grbgetkey.exe
C:\gurobi902\win64\bin\grbprobe.exe
C:\gurobi902\win64\bin\grbtune.exe
C:\gurobi902\win64\bin\grb_ts.exe
C:\gurobi902\win64\bin\gurobi.bat
C:\gurobi902\win64\bin\gurobi.env
C:\gurobi902\win64\bin\gurobi90.dll
C:\gurobi902\win64\bin\Gurobi90.NET.dll
C:\gurobi902\win64\bin\Gurobi90.NET.XML
C:\gurobi902\win64\bin\gurobi90_light.dll
C:\gurobi902\win64\bin\GurobiJni90.dll
C:\gurobi902\win64\bin\gurobi_cl.exe
C:\gurobi902\win64\bin\pysetup.bat
C:\gurobi902\win64\bin\vslauncher.exe
C:\gurobi902\win64\bin\vswhere.exe
We were looking for (but could not find) a file named like
libgurobiXXX.so, libgurobiXXX.dylib, or gurobiXXX.dll. You
should update your GUROBI_HOME environment variable to point to the
correct location.
Have you tried to look for the specific dll in your hard disk and update the GARUBI_HOME accordingly, as per error message? Did you double-check that this specific dll exists on that folder?
In my Ruby script I have to copy one jar file from lib to a different location. Below is the piece of code where I am trying to do so:
FileUtils.mv("#{$HOME_PATH}/lib/myjar1.jar", "#{$HOME_PATH}")
But it is not able to move the jar file to destination. I am seeing the following error:
No such file or directory - file:/home/path/lib/myjar1.jar or file:/home/path/myjar1.jar
I double checked that myjar1.jar is present in source directory. Not sure why I am seeing that error.
I also tried using FileUtils.cp_r("#{$HOME_PATH}/lib/myjar1.jar", "#{$HOME_PATH}") and I am seeing the following error: unknown file type: file:/home/path/lib/myjar1.jar.
Any guidance in copying or moving a jar file is appreciated.
Im assuming you are starting from your home directory (hence the $HOME_PATH). I prefer to use the given ENV hash in IRB.
In IRB this works in MAC OSX:
>> FileUtils.mv("#{ENV['HOME']}/Desktop/my.jar", "#{ENV['HOME']}")
0
The FileUtils#mv method returns 0 as that is the return code of the Unix version of mv which just means it was successful.
After wasting some time to figure out what goes wrong, I finally have to ask for help. I want to use appledocs from Gentle Bytes. I followed every step of the quick install guide, but I´m not able to compile the project.
Here is what I´ve done:
1. cloned it from git://github.com/tomaz/appledoc.git
2. installed the templates to ~/Library/Application Support/appledoc
3. tried to compile the project
Everytime I try to compile, I get following error:
ERROR: AppledocException: At least one directory or file name path is required, use 'appledoc --help'
What do I have to do now?
Sounds like you've compiled it just fine and are now running the program. If it's a command-line program try command-option-R in Xcode to provide some arguments (i.e. names of files that you want to process).
The error means you didn't give it source paths: after all switches, you must give it at least one path to your source files. Can be either file or directory. In later case it will recursively scan the dir. Here's example
appledoc <options> ~/MyProject
Above example will use ~/MyProject directory as a source. You can also add multiple source paths. Note that you need to give the tool few options, see this page for minimum command line and other usage examples.
You either have to copy appledoc executable to one of directories in your path, as suggested by Caleb, or use full path to it when invoking (for example: /path/to/appledoc)
I've setup a custom configuration file for Pylint (name, conveniently, config). There has to be a way that I don't have to include --rcfile=config on every run. How can I set the config file permanently?
When you do not specify the --rcfile option, Pylint searches for a configuration file in the following order and uses the first one it finds:
pylintrc in the current working directory
If the current working directory is in a Python module, Pylint
searches up the hierarchy of Python modules until it finds a
pylintrc file. This allows you to specify coding standards on a
module-by-module basis. Of course, a directory is judged to be a
Python module if it contains an __init__.py file.
The file named by environment variable PYLINTRC
.pylintrc in your home directory, unless you have no home directory
or your home directory is /root
.pylintrc in the current working directory
/etc/pylintrc
Thus depending on the method you choose, Pylint can use a different configuration file based on the location of the code, the user or the machine.
Note that the configuration file only applies to Python files that are in modules. Thus, Pylint still uses its default rules when analyzing Python files in a directory with no __init__.py file.
For example, I have a bin/ directory containing command line applications. Ordinarily, this directory needs no __init__.py file because it is never imported. I had to add a bin/__init__.py file to get Pylint to analyze these Python files using my pylintrc file.
set the path to that file in the PYLINTRC environment variable, or rename the file $HOME/.pylintrc or /etc/pylintrc (the latter is probably only supported on *nix)
It can be done using .pre-commit-config.yaml. This snippet below need to be added to .pre-commit-config.yaml:
repos:
- repo: local
hooks:
- id: pylint
name: pylint
entry: pylint
language: system
types: [python]
args: [
"-rn", # Only display messages
"-sn", # Don't display the score
"--rcfile=.pylintrc", # Link to your config file
"--load-plugins=pylint.extensions.docparams", # Load an extension
]