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2019-10-01Preparation phase added before final buildingMohammad Akhlaghi-136/+0
In many real-world scenarios, `./project make' can really benefit from having some basic information about the data before being run. For example when quering a server. If we know how many datasets were downloaded and their general properties, it can greatly optmize the process when we are designing the solution to be run in `./project make'. Therefore with this commit, a new phase has been added to the template's design: `./project prepare'. In the raw template this is empty, because the simple analysis done in the template doesn't warrant it. But everything is ready for projects using the template to add preparation phases prior to the analysis.
2019-07-28Single wrapper instead of old ./configure, Makefile and ./for-groupMohammad Akhlaghi-6/+6
Until now, to work on a project, it was necessary to `./configure' it and build the software. Then we had to run `.local/bin/make' to run the project and do the analysis every time. If the project was a shared project between many users on a large server, it was necessary to call the `./for-group' script. This way of managing the project had a major problem: since the user directly called the lower-level `./configure' or `.local/bin/make' it was not possible to provide high-level control (for example limiting the environment variables). This was especially noticed recently with a bug that was related to environment variables (bug #56682). With this commit, this problem is solved using a single script called `project' in the top directory. To configure and build the project, users can now run these commands: $ ./project configure $ ./project make To work on the project with other users in a group these commands can be used: $ ./project configure --group=GROUPNAME $ ./project make --group=GROUPNAME The old options to both configure and make the project are still valid. Run `./project --help' to see a list. For example: $ ./project configure -e --host-cc $ ./project make -j8 The old `configure' script has been moved to `reproduce/software/bash/configure.sh' and is called by the new `./project' script. The `./project' script now just manages the options, then passes control to the `configure.sh' script. For the "make" step, it also reads the options, then calls Make. So in the lower-level nothing has changed. Only the `./project' script is now the single/direct user interface of the project. On a parallel note: as part of bug #56682, we also found out that on some macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set to blank. This is no problem because RPATH is automatically set in macOS and the executables and libraries contain the absolute address of the libraries they should link with. But having `DYLD_LIBRARY_PATH' can conflict with some low-level system libraries and cause very hard to debug linking errors (like that reported in the bug report). This fixes bug #56682.
2019-06-13Permission flags of top.mk set to 644 like others, not 755Mohammad Akhlaghi-0/+0
Until now, for some reason, the permission flags of `top.mk' were 755 (good for an executable), not 644 (which is what they should be for a plain text file that is run by another program). This is corrected with this commit.
2019-05-21ImageMagick is now included into the projectRaul Infante-Sainz-0/+0
With this commit, ImageMagick software has been added into the project. This software is useful to deal and treat images from the command line. Since it is widely used and a lot of other programs rely on it, it is worth to have it into the project.
2019-04-30End-of-line Backslashs no longer right under each otherMohammad Akhlaghi-8/+8
When we need to quote the new-line character we end the line with a backslash (`\'). Until now, our convention has been to put all such backslashes under each other to help in visual inspection. But this causes a lot of confusion in version control: if only one line's length is larger, the whole block will be marked as changed and thus makes it hard to visually see the actual change. It also makes debuging the code (adding some temporary lines) hard. With this commit, I went through all the files and tried to fix all such cases so only a single white space character is between the last command character and the backslash. Where there was an empty line (ending with a backslash, to help in visually separating the code into blocks), I put the backslash right under the previous line's. This completes task #15259.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-0/+136
Until now, the software building and analysis steps of the pipeline were intertwined. However, these steps (of how to build a software, and how to use it) are logically completely independent. Therefore with this commit, the pipeline now has a new architecture (particularly in the `reproduce' directory) to emphasize this distinction: The `reproduce' directory now has the two `software' and `analysis' subdirectories and the respective parts of the previous architecture have been broken up between these two based on their function. There is also no more `src' directory. The `config' directory for software and analysis is now mixed with the language-specific directories. Also, some of the software versions were also updated after some checks with their webpages. This new architecture will allow much more focused work on each part of the pipeline (to install the software and to run them for an analysis).