frozen.md 3.2 KB
Newer Older
Yohan Jarosz's avatar
Yohan Jarosz committed
1
2
3
4
5
6
7
8
9
10
11
12
13
---
# You don't need to edit this file, it's empty on purpose.
# Edit theme's home layout instead if you wanna make some changes
# See: https://jekyllrb.com/docs/themes/#overriding-theme-defaults
layout: frozen
title: frozen
order: 4
---

{: .rtitle}
<div>
## IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

Elisabeth Guerard's avatar
Elisabeth Guerard committed
14
Please cite the article on [Genome Biology][urlGenomeBiology].
Yohan Jarosz's avatar
Yohan Jarosz committed
15
16
17
Shaman Narayanasamy†, Yohan Jarosz†, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes*
</div>

Elisabeth Guerard's avatar
Elisabeth Guerard committed
18
19
{: .rgridblock}
<div>
Yohan Jarosz's avatar
Yohan Jarosz committed
20
21
{: .rblock}
<div>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
22
### <i class="fas fa-globe"></i> Website
Yohan Jarosz's avatar
Yohan Jarosz committed
23
<hr>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
24
The **IMP** website hosted within *R3lab* frame is available [here][urlIMP].
Yohan Jarosz's avatar
Yohan Jarosz committed
25
26
27
28
</div>

{: .rblock}
<div>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
29
### <i class="fas fa-code"></i> Source code
Yohan Jarosz's avatar
Yohan Jarosz committed
30
<hr>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
31
The source code of IMP is available on the [LCSB Gitlab][urlGitIMP] where you can traceback what have been done by the authors.
Yohan Jarosz's avatar
Yohan Jarosz committed
32
33
34
35
36
</div>


{: .rblock}
<div>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
37
### <i class="fas fa-code"></i> Additionnal source code
Yohan Jarosz's avatar
Yohan Jarosz committed
38
<hr>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
39
Some additionnal analysis made on the paper as also available on the [LCSB Gitlab][urlGitIMPDoc].
Yohan Jarosz's avatar
Yohan Jarosz committed
40
41
42
43
</div>

{: .rblock}
<div>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
44
### <i class="fas fa-cogs"></i> Workflow
Yohan Jarosz's avatar
Yohan Jarosz committed
45
<hr>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
46
Snakemake, a reproducible workflow engine that allow us IMP users execute the same workflow for each analysis. From [Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.][urlBioinformatic]
Yohan Jarosz's avatar
Yohan Jarosz committed
47
48
49
50
</div>

{: .rblock}
<div>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
51
### <i class="fas fa-dolly-flatbed"></i> Tool repository
Yohan Jarosz's avatar
Yohan Jarosz committed
52
<hr>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
53
The **IMP** tool repository is hosted on the [LCSB webdav storage][urlWebdavIMP]. You will find some of the tools installed within IMP. IMP versions are stored under the dist folder.
Yohan Jarosz's avatar
Yohan Jarosz committed
54
55
56
57
</div>

{: .rblock}
<div>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
58
### <i class="fab fa-docker"></i> Environment
Yohan Jarosz's avatar
Yohan Jarosz committed
59
<hr>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
60
All tools dependencies of IMP are frozen inside a docker container. The files used to build the container can be found on Gitlab and versioned tarballs of the containers are found under the [webdav][urlWebdavIMPDep].
Yohan Jarosz's avatar
Yohan Jarosz committed
61
62
63
64
</div>

{: .rblock}
<div>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
65
### <i class="fas fa-wrench"></i> R toolkit
Yohan Jarosz's avatar
Yohan Jarosz committed
66
<hr>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
67
We use the [checkpoint][urlLibraryCheck] library to ensure that all of the necessary R packages are installed with the correct versions.
Yohan Jarosz's avatar
Yohan Jarosz committed
68
69
70
71
</div>

{: .rblock}
<div>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
72
### <i class="fas fa-book"></i> Report
Yohan Jarosz's avatar
Yohan Jarosz committed
73
<hr>
Elisabeth Guerard's avatar
Elisabeth Guerard committed
74
75
76
77
78
79
80
81
82
83
84
85
86
 **IMP** report contains all information needed to reproduce the same workflow, from the version of **IMP** used to make the analysis to the configuration file used to start the workflow. Everything is condensed and organized within an HTML report. Some reports can be found [here][urlIMPReport].
</div>
</div>

[urlIMP]:https://imp.pages.uni.lu/web/
[urlGenomeBiology]:https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1116-8
[urlGitIMP]:https://git-r3lab.uni.lu/IMP/IMP
[urlGitIMPDoc]:https://git-r3lab.uni.lu/IMP/IMP_manuscript_analysis
[urlBioinformatic]:https://academic.oup.com/bioinformatics/article/28/19/2520/290322
[urlWebdavIMP]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/
[urlWebdavIMPDep]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/dist/
[urlLibraryCheck]:https://cran.r-project.org/web/packages/checkpoint/vignettes/checkpoint.html
[urlIMPReport]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/reports/