Update README.md

Update install info to reflect move to portable version (#56). Add contact info.

README.md

@@ -8,22 +8,20 @@
 
 * `qc_rel.py`: runs QC for family GWAS data. Designed to be consistent with ricopili trio QC, with minor adjustments to mendelian error handling and streamlined output.
 * `pca_rel.py`: main driver script to run PCA on family GWAS data. Includes strict QC (with LD pruning, etc), extraction of a set of unrelated individuals to compute PCs, and projection of PCA to full dataset. Jobs are submitted via UGER, and ricopili-like success/failure emails are sent on completion. See tasks `strict_qc.py` and `imus_pca.py`.
-* `admix_rel.py`: estimates relatedness for admixed samples. Relatedness is estimated by starting with a subset of individuals who are unrelated, running an Admixture analysis, selecting "exemplar" individuals for each ancestry component, using those individuals to anchor a supervised Admixture analysis fo the full data, and using those Admixture results as the basis for ancestry-adjusted relatedness estimation using REAP.
+* `admix_rel.py`: estimates relatedness for admixed samples. Relatedness is estimated by starting with a subset of individuals who are unrelated, running an Admixture analysis, projecting that Admixture solution to the remaining samples, and using those Admixture results as the basis for ancestry-adjusted relatedness estimation using REAP.
 * `filter_ped.py`: uses genetic relatedness information to flag (a) cryptic relatedness across FIDs, (b) unrelated individuals within FIDs, (c) possible parent/offspring pair not identified in .fam file, and (d) parent/offspring pairs indicated by pedigree that aren't supported by genetic relatedness. Provides a suggested sample exclusion list based on weighted preferences for phenotype, pedigree, and genotyping rate.
 * `ped_confirm.py`: confirms that reported pedigrees in .fam file are consistent with genetic relatedness. Works as a wrapper to `find_expected_pedigree.pl` from PRIMUS.
-* `gwas_rel.py`: Genome-wide association analysis (in parallelized chunks) with either `plink --dfam` or a GEE model.
+* `gwas_rel.py`: Genome-wide association analysis (in parallelized chunks) with either `plink --dfam`, a GEE model, or a logistic mixed model (using GMMAT).
 * `impute_rel.py`: Imputation pipeline for related samples using SHAPEIT's `--duohmm` and IMPUTE2. Includes build check (with liftOver if needed), alignement to reference, phasing, imputation, and best-guess genotype calls with MAF/info score/mendelian error filtering.
 
 
 ### Installation at Broad
 
 ##### 1. The following assumes:
 
-* You're working on the Broad UGER cluster (though can probably be adapted)
-* You've already installed [ricopili](https://github.com/Nealelab/ricopili).
 * You have git configured with a github account.
-
-Note additional dependencies may exist for some modules (e.g. Admixture, REAP, PRIMUS).
+* You have dependencies installed, or can install them (e.g. Admixture, REAP, PRIMUS).
+* You're either on one of the default clusters (Broad, Lisa) or can define appropriate configuation files for your local compute environment (see step 6).
 
 ##### 2. Download picopili from github
 
@@ -33,31 +31,34 @@ cd ~/github
 git clone https://github.com/Nealelab/picopili.git
 ```
 
-##### 3. Add picopili to search path
+##### 3. Run the configuration scripts
+
+```
+cd picopili
+./CONFIG
+./GET_REFS
+```
+Follow on screen instructions for each script. If dependencies are missing or need to be adjusted, see `~/.picopili.conf`.
+
+##### 4. Add picopili to search path
 
 In `~/.my.bashrc` (or equivalent for your shell) add the line:
 
 ```
 PATH=$HOME/github/picopili/rp_bin:$PATH
 ```
 
-##### 4. Logout and log back in.
+##### 5. Logout and log back in.
 
 Applies the changes in `~/.my.bashrc`.
 
+##### 6. Define cluster configuration
 
-### Installation on other platforms
+You will also need to define a cluster configuration with a `.conf` configuation file and a `.sub.sh` sumbission script template. See `./picopili/cluster_templates/` for examples for a SGE/UGE job system (`broad_uger.*`) and for a TORQUE/Maui job system with tasks parallelized within node as well as across nodes (`lisa.*`).
 
-For other platforms, please see the `portable` branch (https://github.com/Nealelab/picopili/tree/portable), with patch notes in pull #56.
 
-Briefly, you will want to clone from github and switch to the portable branch:
-```
-mkdir ~/github
-cd ~/github
-git clone https://github.com/Nealelab/picopili.git
-git checkout portable
-```
+### Contact
 
-Then run `./picopili/CONFIG` and `./picopili/GET_REFS` to setup the installation. 
+Bug report? Open an issue right here on github!
 
-You will also need to define a cluster configuration with a `.conf` configuation file and a `.sub.sh` sumbission script template. See `./picopili/cluster_templates/` for examples for a SGE/UGE job system (`broad_uger.*`) and for a TORQUE/Maui job system with tasks parallelized within node as well as across nodes (`lisa.*`).
+Questions? Feedback? Email the authors. (rwalters at broad)