On previous versions of Snakemake (tested on 3.9.1 using integration with bioconda --use-conda) I could just check for the md5 hash of the environment.yaml file and find the respective environment at: workdir/.snakemake/conda/md5
On version 4.3.0 the md5 hash of the file does not match the environment folder. Looking at the source code I found out that the full path of the environment file is included when calculating the md5 hash to avoid conda errors on hard-coded paths but I am not sure how to generate the correct hash.
Is there another easier way to get the environment path inside a rule? If not, how can I generate the correct md5 to finde the environment?
Currently, the only reasonable way is to check the log. The path is displayed when the environment is activated. However, it is a very good idea to provide a command line option to list all environments, something like snakemake --list-conda-envs. I will do that as soon as possible.
EDIT: I have implemented --list-conda-envs in the master branch. It will be in the next release.
Related
Trying to get the sidekick image built and having some issues. Is there any documentation other than the README.md file?
My current problem is with getting the JRE requirement working but there are others. The page says "download Oracle JRE and place it inside the working directory. Optionally if you have a company wide distribution url, use that one at a later step." and the help says "Java (JRE) download url or path inside working directory". Have not been able to get this to work.
I went to the JRE link provided and was presented with options to download a rpm file or a tar.gz file. Which is expected (was unable to get either one working)?
It says to place the file in the "working directory" but not sure where exactly. Tried in sidekick folder and in sidekick/jre both without success no matter what I used after the -j command. Is this just the path or should the filename be included as well? Can I get an example?
I'm running this script using my login but noticed the output folder is being created with root user and group. I see no indication that this should be run with sudo. What is the correct way to run this script?
Using debug, I see the function "download if not cached". Can I save these files (JRE, Bamboo jar file, etc.) somewhere so I don't have to worry about downloading them? If so, where should they go? Looks like I might have a problem with the wget to d/l the jar file so would like to just be able to place all these in a folder and be done with it.
It looks like the major problem is the script didn't clean up after itself if it fails. The issue was the first time it failed then that caused subsequent issues as the output folder was already there. Removing this directory between each attempt help.
As for the correct syntax for the -j JRE option I manually downloaded the JRE and placed in a folder called per-build-container/sidekick/stuff/. For the command line it is not just the path but the file name as well (the tar.gz and not the RPM). For my case it was
-j stuff/jre-8u251-linux-x64.tar.gz
Note I also ran the script as sudo. Wasn't stated but seemed to work OK.
Another issue I ran into was the download of the agent jar file. There is a redirect in the wget file that was not working for us. I ended up editing the script and replacing the Altassian based url with the redirected one.
This addresses all the issues I ran into with the initial question.
I am installing a package manually on my own system because I need to make some changes to it that aren't available in the basic version in my package manager. I also am trying to keep packages installed locally if possible, so I'm installing it with prefix=$HOME/.local instead of the more common prefix=/usr/local.
When I do this, I have no problem executing the program from my terminal, because I added ~/.local/bin to my PATH and the package was installed with relative paths to its shared libraries (i.e. ~/.local/lib/<package>). Executing from the command line is no problem, but I want to be able to access it from the favorites menu in gnome, and for that I need to make use of the <package>.desktop file.
I could hard-code the path to the executable in the .desktop file itself, but when I pull a later version down and re-install it, I'll have to redo those steps. I was wondering if there's a way to avoid that.
I've tried symlinking the executable to a directory where .desktop files do have included in their path, and the application is correctly treated as a GUI option, but launching the executable results in an error trying to find a shared library. I think this has to do with how cmake handles rpaths, which to my understanding is a way of relatively linking executables with their required libraries.
I think what I want to do is have PATH inside a .desktop file include ~/.local/bin, without changing the .desktop file itself. Can I alter the 'default' path used in accessing a .desktop file?
The answer to my question was found in the Archwiki:
Specifically, I needed to add ~/.local/bin to my path in ~/.xinitrc. Now my graphical programs work as expected.
I am developing a library which uses CMake to control it. It would be good to provide a "FindXXX.cmake" which locates the library and header files. This file would enable the users to use the command "find_package(XXX)" to find my library.
However, I don't know how to install my lib's "FindXXX.cmake" to an correct location. I failed to find a CMake's build-in mechanism to install a "FindXXX.cmake". In addition, CMake's variable "CMAKE_MODULE_PATH" is a list of directories, so I cannot install according to that vairable because I cannot decide which specific directory to use.
If the copy of CMake is installed to a standard location(i.e. use no prefix etc) then this can be done by placing the file in /usr/share/cmake/Modules/ directory.
If you are going to supply a bundle probably you can add some commands to check if the cmake is available. if yes you can check for cmake --system-information|grep _INCLUDED_SYSTEM_INFO_FILE value from that to get modules directory.
Otherwise there's no way you can do that.
A workaround can be done i.e. if there is a binary in your bundle then you can add a command line option for placing this file.
I'm having an issue with linked Resources in Flash Builder. I work in a team environment where we use Linked Resources extensively. We just started developing ANEs and noticed that while linkedResources are used in the libraryPathEntry, in the buildTargets like anePathEntry and airCertificatePath, the absolute path is stored. I tried editing the .actionScriptProperties files directly, modifying the buildtarget absolute paths to linked resource equivalents using the libraryPathEntry as a guide but FlashBuilder complained when loading the project.
Is there a way to get the buildTargets to respect linkedResources and not save the absolute path? I'm trying to avoid the draconian way where all developers must have the exact same directory structure.
Thanks!
Randy
My team had this exact problem and all attempts to fix it with relative paths or workspace macros (i.e. ${PROJECT_LOC}) failed. It seems as if the team in charge of Flash Builder neglected to support relative paths in these particular dialogs, despite them being supported elsewhere.
Here is what we have done to fix this problem. I am assuming you are on a Mac/Linux or the like. If not, the concept here can still be applied.
Most of our projects already have a "set up" bash script that contributors run when they get code. Inside of that script, we simply set up a couple of symbolic links from the user specific absolute path, to a new absolute path with a "common" user. The script first creates the directory if it does not exist, and then creates the symlinks.
sudo mkdir -p /Users/common/<project>/
sudo ln -f -h -s ~/path/to/certificate/dir /Users/common/<project>/certificates
Obviously you can use whatever you like and whatever makes sense for the common path.
Now, in your .actionScriptProperties file you can change the location pointed to by the provisingFile and airCertificatePath to this new common absolute path.
<buildTarget ... provisioningFile="/Users/common/<project>/certificates/provisionfile.mobileprovision" ... >
<airSettings airCertificatePath="/Users/common/<project>/certificates/cert.p12" ... >
We actually take this a step further (and I suspect you will need to also) and create common symlink paths for the ANE files themselves. This ends up changing the anePathEntry to the common path as well.
<anePathEntry path="/Users/common/<project>/anes/some.ane"/>
You will need to make sure that you either hand edit the .actionScriptProperties file directly, or type in the fully qualified symlink path into the dialogs directly. Any attempt at using the Finder dialog launched by Flash Builder to navigate to the files in the common location resulted in the symlinks being auto-resolved to their actual locations.
The script requires sudo, which as I'm sure you know, will require that the users of it know their root password. Maybe some more bash savvy folks can suggest a way around sudo if this is not an option for you.
This will work for android stuff as well I believe. I don't know if that matters to you or not.
Hope this helps!
It looks like this issue was called out in the Flash Builder 4.6 known issues:
http://helpx.adobe.com/flash-builder/kb/flash-builder-4-6-known.html
https://bugs.adobe.com/jira/browse/FB-32955
The bug is apparently fixed but I haven't been able to check the new Flash Builder 4.7 beta yet:
http://blogs.adobe.com/flex/2012/08/flash-builder-4-7-beta-is-here.html
How can I modify the mercurial.ini file to include an environment variable such as %userprofile%.
Specific situation:
I am learning to use Mercurial. I have modified the [ui] section of Mercurial.ini (in my home path) to include:
ignore = c:\users\user\.hgignore
Where user is my username literal. The .hgignore file includes filename filters that are used to ignore files during commit. How can I alter it from being the a literal user to an environment variable $user?
It won't interpolate environment variables in the hgrc, but I do believe that tilda expands to your home/profile directory correctly even on windows.
So:
ignore = ~/.hgignore
should work on windows and elsewhere (even the slashes get spun the wrong way automatically for you).
For other variables you'd need to get a little tricker and write a batch/cmd file that does the interpolation in advance and then hands the result off to mercurial for processing.
The mercurial.ini parses the environment variables just fine.
From my mercurial.ini:
[ui]
ignore = %USERPROFILE%/.hgignore
Works like a charm. Windows 7 Ultimate x64, Mercurial 1.5 (binary installation). The hgignore file is honored both my the command line hg.exe, and tortoiseHG.