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| .. | | 03-May-2022 | - |
| config/ | H | 10-May-2019 | - | 2,283 | 1,536 |
| htslib/ | H | 03-May-2022 | - | 54,237 | 36,669 |
| scripts/ | H | 03-May-2022 | - | 2,718 | 1,873 |
| src/ | H | 10-May-2019 | - | 54,462 | 37,181 |
| tests/ | H | 10-May-2019 | - | 280 | 192 |
| ChangeLog | H A D | 09-May-2019 | 85.5 KiB | 1,399 | 1,285 |
| INSTALL | H A D | 24-Sep-2015 | 9.3 KiB | 237 | 179 |
| LICENSE | H A D | 24-Sep-2015 | 34.3 KiB | 675 | 553 |
| Makefile.am | H A D | 27-Feb-2019 | 4.6 KiB | 121 | 99 |
| Makefile.in | H A D | 09-May-2019 | 61.6 KiB | 1,682 | 1,524 |
| README | H A D | 24-Dec-2018 | 1 KiB | 44 | 26 |
| acinclude.m4 | H A D | 02-Oct-2016 | 13.5 KiB | 563 | 446 |
| aclocal.m4 | H A D | 09-May-2019 | 40 KiB | 1,132 | 1,032 |
| autogen.sh | H A D | 24-Sep-2015 | 186 | 6 | 4 |
| config.h.in | H A D | 09-May-2019 | 3.5 KiB | 136 | 92 |
| configure | H A D | 09-May-2019 | 230.1 KiB | 8,345 | 6,871 |
| configure.ac | H A D | 09-May-2019 | 2.9 KiB | 102 | 87 |
README
1The Stacks Pipeline
2-------------------
3
40. Prerequisites
5
6Stacks should build on any standard UNIX-like environment (Apple OS X, Linux,
7etc.) Stacks is an independent pipeline and can be run without any additional
8external software.
9
10If compiling with the standard GCC compiler, Stacks needs a version of the compiler
11newer than GCC 4.9.0.
12
131. Build the software. Stacks uses the standard autotools install:
14
15% tar xfvz stacks-x.xx.tar.gz
16% cd stacks-x.xx
17% ./configure
18
19You can change the root of the install location (/usr/local/ on most
20operating systems) by specifying the --prefix command line option to
21the configure script.
22
23% ./configure --prefix=/home/smith/local
24
25You can enable Sparsehash by adding the following options:
26
27% ./configure --enable-sparsehash
28
29% make
30
31You can speed up the build if you have more than one processor:
32
33% make -j 8
34
353. Install the software.
36
37% sudo make install
38
39A default Stacks install will install files in the following way:
40
41/usr/local/bin - stacks executables and perl scripts
42
43The pipeline is now ready to run.
44