miga-base 1.2.17.1 → 1.2.17.3

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd

@@ -7,20 +7,24 @@
 enve.recplot2.findPeaks.__emauto_one(x, comp, do_crit, best, verbose, ...)
 }
 \arguments{
-\item{x}{\code{\link{enve.RecPlot2}} object}
+\item{x}{\code{\link{enve.RecPlot2}} object.}
 
-\item{comp}{Components}
+\item{comp}{Components.}
 
-\item{do_crit}{Function estimating the criterion}
+\item{do_crit}{Function estimating the criterion.}
 
-\item{best}{Best solution thus far}
+\item{best}{Best solution thus far.}
 
-\item{verbose}{If verbose}
+\item{verbose}{If verbose.}
 
-\item{...}{Additional parameters for \code{\link{enve.recplot2.findPeaks.em}}}
+\item{...}{Additional parameters for \code{\link{enve.recplot2.findPeaks.em}}.}
+}
+\value{
+Updated solution with the same structure as \code{best}.
 }
 \description{
-Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.emauto}}).
+Internal ancillary function (see
+\code{\link{enve.recplot2.findPeaks.emauto}}).
 }
 \author{
 Luis M. Rodriguez-R [aut, cre]

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd

@@ -44,8 +44,12 @@ enve.recplot2.findPeaks.__mow_one(
 
 \item{log}{If log-transformed depths}
 }
+\value{
+Return an \code{enve.RecPlot2.Peak} object.
+}
 \description{
-Internall ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
+Internal ancillary function (see
+\code{\link{enve.recplot2.findPeaks.mower}}).
 }
 \author{
 Luis M. Rodriguez-R [aut, cre]

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd

@@ -9,6 +9,9 @@ enve.recplot2.findPeaks.__mower(peaks.opts)
 \arguments{
 \item{peaks.opts}{List of options for \code{\link{enve.recplot2.findPeaks.__mow_one}}}
 }
+\value{
+A list of \code{enve.RecPlot2.Peak} objects.
+}
 \description{
 Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
 }

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd

@@ -9,8 +9,8 @@ enve.recplot2.findPeaks.mower(
   min.points = 10,
   quant.est = c(0.002, 0.998),
   mlv.opts = list(method = "parzen"),
-  fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1, 0.5, 0.8), start =
-    list(omega = 1, alpha = -1), lower = c(0, -Inf, -Inf)),
+  fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1, 0.5, 0.8), start
+    = list(omega = 1, alpha = -1), lower = c(0, -Inf, -Inf)),
   fitdist.opts.norm = list(distr = "norm", method = "qme", probs = c(0.4, 0.6), start =
     list(sd = 1), lower = c(0, -Inf)),
   rm.top = 0.05,

data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd

@@ -14,9 +14,9 @@ enve.recplot2.windowDepthThreshold(
 \arguments{
 \item{rp}{Recruitment plot, an \code{\link{enve.RecPlot2}} object.}
 
-\item{peak}{Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to be a
-list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core peak is
-used (see \code{\link{enve.recplot2.corePeak}}).}
+\item{peak}{Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to
+be a list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core
+peak is used (see \code{\link{enve.recplot2.corePeak}}).}
 
 \item{lower.tail}{If \code{FALSE}, it returns windows significantly above the peak in
 sequencing depth.}

data/utils/enveomics/enveomics.R/man/enve.tribs.Rd

@@ -50,8 +50,8 @@ It must be a matrix or matrix-coercible object, with samples as rows and
 dimensions as columns.}
 
 \item{pre.tribs}{Optional. If passed, the points are recovered from this object (except if
-\code{points} is also passed. This should be an \code{\link{enve.TRIBS}} object 
-estimated on the same objects (the selection is unimportant).}
+\code{points} is also passed. This should be an \code{\link{enve.TRIBS}}
+object estimated on the same objects (the selection is unimportant).}
 }
 \value{
 Returns an \code{\link{enve.TRIBS}} object.

data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd

@@ -70,6 +70,9 @@ model?}
 
 \item{...}{Any other graphic parameters.}
 }
+\value{
+No return value.
+}
 \description{
 Plots an \code{\link{enve.GrowthCurve}} object.
 }

data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd

@@ -38,6 +38,9 @@ as areas, and plots the outliers as points.}
 
 \item{...}{Any additional parameters supported by \code{plot}.}
 }
+\value{
+No return value.
+}
 \description{
 Plot an \code{\link{enve.TRIBS}} object.
 }

data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd

@@ -19,9 +19,9 @@
 \arguments{
 \item{x}{\code{\link{enve.TRIBStest}} object to plot.}
 
-\item{type}{What to plot. \code{overlap} generates a plot of the two contrasting empirical
-PDFs (to compare against each other), \code{difference} produces a plot of the
-differences between the empirical PDFs (to compare against zero).}
+\item{type}{What to plot. \code{overlap} generates a plot of the two contrasting
+empirical PDFs (to compare against each other), \code{difference} produces a
+plot of the differences between the empirical PDFs (to compare against zero).}
 
 \item{col}{Main color of the plot if type=\code{difference}.}
 
@@ -37,6 +37,9 @@ differences between the empirical PDFs (to compare against zero).}
 
 \item{...}{Any other graphical arguments.}
 }
+\value{
+No return value.
+}
 \description{
 Plots an \code{\link{enve.TRIBStest}} object.
 }

data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd

@@ -17,8 +17,8 @@
   id.lim = range(x$id.breaks),
   pos.lim = range(x$pos.breaks),
   pos.units = c("Mbp", "Kbp", "bp"),
-  mar = list(`1` = c(5, 4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1), 1, 5), 4, 4, 1)
-    + 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 4), 1, 2) + 0.1, `4` =
+  mar = list(`1` = c(5, 4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1), 1, 5), 4, 4,
+    1) + 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 4), 1, 2) + 0.1, `4` =
     c(ifelse(any(layout == 1), 1, 5), ifelse(any(layout == 2), 1, 4), 4, 2) + 0.1, `5` =
     c(5, 3, 4, 1) + 0.1, `6` = c(5, 4, 4, 2) + 0.1),
   pos.splines = 0,

data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd

@@ -11,6 +11,9 @@
 
 \item{...}{No additional parameters are currently supported.}
 }
+\value{
+No return value.
+}
 \description{
 Summary of an \code{\link{enve.GrowthCurve}} object.
 }

data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd

@@ -11,6 +11,9 @@
 
 \item{...}{No additional parameters are currently supported.}
 }
+\value{
+No return value.
+}
 \description{
 Summary of an \code{\link{enve.TRIBS}} object.
 }

data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd

@@ -11,6 +11,9 @@
 
 \item{...}{No additional parameters are currently supported.}
 }
+\value{
+No return value.
+}
 \description{
 Summary of an \code{\link{enve.TRIBStest}} object.
 }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.17.1
+  version: 1.2.17.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-02-14 00:00:00.000000000 Z
+date: 2023-02-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -315,41 +315,6 @@ files:
 - utils/enveomics/Manifest/categories.json
 - utils/enveomics/Manifest/examples.json
 - utils/enveomics/Manifest/tasks.json
-- utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash
-- utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl
-- utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl
-- utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl
-- utils/enveomics/Pipelines/assembly.pbs/README.md
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME.bash
-- utils/enveomics/Pipelines/assembly.pbs/kSelector.R
-- utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
-- utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
-- utils/enveomics/Pipelines/assembly.pbs/soap.pbs
-- utils/enveomics/Pipelines/assembly.pbs/stats.pbs
-- utils/enveomics/Pipelines/assembly.pbs/velvet.pbs
-- utils/enveomics/Pipelines/blast.pbs/01.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/02.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/03.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl
-- utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash
-- utils/enveomics/Pipelines/blast.pbs/FastA.split.pl
-- utils/enveomics/Pipelines/blast.pbs/README.md
-- utils/enveomics/Pipelines/blast.pbs/RUNME.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.check.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.run.bash
-- utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
-- utils/enveomics/Pipelines/idba.pbs/README.md
-- utils/enveomics/Pipelines/idba.pbs/RUNME.bash
-- utils/enveomics/Pipelines/idba.pbs/run.pbs
-- utils/enveomics/Pipelines/trim.pbs/README.md
-- utils/enveomics/Pipelines/trim.pbs/RUNME.bash
-- utils/enveomics/Pipelines/trim.pbs/run.pbs
 - utils/enveomics/README.md
 - utils/enveomics/Scripts/AAsubs.log2ratio.rb
 - utils/enveomics/Scripts/Aln.cat.rb
@@ -493,6 +458,7 @@ files:
 - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv
 - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim
 - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec
+- utils/enveomics/Tests/low-cov.bg.gz
 - utils/enveomics/Tests/phyla_counts.tsv
 - utils/enveomics/Tests/primate_lentivirus.ogs
 - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm

data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash

@@ -1,69 +0,0 @@
-#!/bin/bash
-
-##################### VARIABLES
-# Queue: Preferred queue.  Delete (or comment) this line to allow
-# automatic detection:
-#QUEUE="biocluster-6"
-# If you set the QUEUE variable, you MUST set the WTIME variable
-# as well, containing the walltime to be asked for.  The WTIME
-# variable is ignored otherwise.
-WTIME="120:00:00"
-
-# Scratch:  This is where the output will be created.
-SCRATCH="$HOME/scratch/pipelines/assembly"
-
-# Data folder:  This is the folder that cointains the input files.
-DATA="$HOME/data/trim"
-
-# Location of Newbler's binaries
-BIN454="$HOME/454/bin"
-
-# Name(s) of the library(ies) to use, separated by spaces:
-# This is determined by the name of your input files.  For example,
-# if your input files are: LLSEP.CoupledReads.fa and LWP.CoupledReads.fa,
-# use:
-# LIBRARIES="LLSEP LWP"
-# It's strongly encouraged to use only one per CONFIG file.
-LIBRARIES="A";
-
-# Use .CoupledReads.fa and/or .SingleReads.fa (yes or no):
-USECOUPLED=yes
-USESINGLE=no
-
-# Insert length (in bp):  This is the average length of the entire insert,
-# not just the gap length.
-INSLEN=300
-
-# Number of CPUs to use (for SOAP and Newbler):
-PPN=16
-
-# RAM multiplier: Multiply the estimated required RAM by this number:
-RAMMULT=1
-
-# Maximum number of simultaneous jobs: Uncomment and increase these values if
-# you have increased resources (e.g., a dedicated queue); uncomment and decrease
-# if the resources are scarce (e.g., a very busy queue or other simultaneous jobs).
-#VELVETSIM=22
-#SOAPSIM=8
-
-# Extra parameters for Velvet: Any additional parameters to be passed to
-# velvetg or velveth.  If you have MP data, consider adding the option
-# -shortMatePaired yes to VELVETG_EXTRA.  If you have Nextera, consider
-# adding the option above, plus the option -ins_length_sd <integer>, to
-# indicate the standard deviation of the insert size.  By default, the
-# SD is assumed to be 10% of the average, but Nextera produces much
-# wider distribution of sizes (i.e., larger SD).  Typically you shouldn't
-# need to add anything in VELVETH_EXTRA.
-VELVETH_EXTRA=""
-VELVETG_EXTRA=""
-
-# Clean non-essential files (yes or no):
-CLEANUP=yes
-
-# Best k-mers:  Space-delimited list of kmers selected from Velvet and SOAP.
-# This is to be modified at the begining of step 4, and it's ignored in all
-# the other steps.
-K_VELVET="21 23 35"
-K_SOAP="21 23 35"
-
-

data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl

@@ -1 +0,0 @@
-../../Scripts/FastA.N50.pl

data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl

@@ -1 +0,0 @@
-../../Scripts/FastA.filterN.pl

data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl

@@ -1 +0,0 @@
-../../Scripts/FastA.length.pl

data/utils/enveomics/Pipelines/assembly.pbs/README.md

@@ -1,189 +0,0 @@
-@author: Luis Miguel Rodriguez-R <lmrodriguezr at gmail dot com>
-
-@update: Mar-17-2013
-
-@license: artistic 2.0
-
-@status: semi
-
-@pbs: yes
-
-# IMPORTANT
-
-This pipeline was developed for the [PACE cluster](http://pace.gatech.edu/).  You
-are free to use it in other platforms with adequate adjustments.  It is largely
-based on Luo _et al._ 2012, ISME J.
-
-# PURPOSE
-
-This pipeline assemblies coupled and/or single reads from one or more libraries.
-It assumes that the reads have been quality-checked and trimmed.
-
-# HELP
-
-1. Files preparation:
-
-   1.1. Copy this folder to the cluster.
-   
-   1.2. Copy the sequences to the cluster.  Only trimmed/filtered reads are used.
-      All the files are expected to be in the same folder, and the filenames must
-      end in `.CoupledReads.fa` or `.SingleReads.fa`.
-   
-   1.3. Copy the file `CONFIG.mock.bash` to `CONFIG.<name>.bash`, where `<name>` is a
-      short name for your run (avoid characters other than alphanumeric).
-   
-   1.4. Change the variables in `CONFIG.<name>.bash`.  Notice that this pipeline
-      supports running several libraries at the same time, but it's strongly
-      recomended to run only one per config file, because the insert length
-      (in step 2) and the selected k-mers (in step 3) are fixed for all the
-      included libraries.  Also, there is a technical consideration:  The first
-      step will execute parallel jobs for each odd number between 21 and 63, and
-      SOAP will use 16 CPUs by default, which means 357 CPUs will be requested
-      per library in step 2.  It's a bad idea to run many libraries at the same
-      time.
-
-   1.5. If you have Mate-paired datasets (for example, prepared with Nextera), first
-      reverse-complement all the reads.  See also the `VELVETG_EXTRA` variable in
-      the `CONFIG.<name>.bash` file.
-
-2. Velvet and SOAP assembly:
-   
-   2.1. Execute `./RUNME-2.bash <name>` in the head node (see [troubleshooting](#troubleshooting) #1).
-   
-   2.2. Monitor the tasks named velvet_* and soap_*.
-   
-   2.3. Once completed, make sure the files .proc contain only the
-      word "done".  To do this, you may execute:
-```
-      grep -v '^done$' *.proc
-```
-
-      If successful, the output of the above command should be empty.  See
-      [Troubleshooting](#troubleshooting) #2 and #3 below if one or more of your jobs failed.
-
-3. K-mers selection:
-   
-   3.1. If you completed step 2, execute `./RUNME-3.bash <name>` in the head
-      node.
-   
-   3.2. Once completed, download and open the files `*.n50.pdf`.
-   
-   3.3. Select the three "best" k-mers for Velvet and for SOAP (they don't
-      have to be the same).  There is no well-tested method to select the
-      "best", and this is why this protocol is not automated, but semi-
-      automated.  A generally good rule-of-thumb is: pick one that optimizes
-      the amount of sequences used (these are the grey bars in the plot;
-      usually this is the smallest k-mer), pick one that optimizes the N50
-      (this is the dashed red line; usually this is a large k-mer), and pick
-      one that optimizes both (something in the middle).  You can select
-      more or less than three k-mers, this is just a suggestion.
-
-4. Newbler assembly:
-   
-   4.1. Edit the file `CONFIG.<name>.bash`: set the variables `K_VELVET` and
-      `K_SOAP` to contain the lists of "best" selected k-mers for Velvet and
-      SOAP, respectively.
-   
-   4.2. Execute `./RUNME-4.bash <name>` in the head node.
-   
-   4.3. Monitor the task newbler_*.  Once finished, your assembly is ready.
-      Once completed, make sure the file .newbler.proc contain only the
-      word "done".  To do this, you may execute:
-```
-      grep -v '^done$' *.proc
-```
-      If successful, the output should be empty.
-   
-   4.4. The final assembly should be located in the `SCRATCH` path, in a folder
-      named `<lib>.newbler/assembly/`.  The file `454AllContigs.fna` contains
-      all the assembled contigs, `454LargeContigs.fna` contains the contigs
-      with 500bp or more in length, and `454NewblerMetrics.txt` contains some
-      relevant statistics.
-
-
-# Comments
-
-* Some scripts contained in this package are actually symlinks to files in the
-  _Scripts_ folder.  Check the existance of these files when copied to
-  the cluster.
-
-# Troubleshooting
-
-1. Do I really have to change directory (`cd`) to the pipeline's folder everytime
-   I want to execute something?
-   
-   No.  Not really.  For simplicity, this file tells you to execute, for example,
-   `./RUNME-2.bash`.  However, you don't really have to be there, you can execute it
-   from any location.  For example, if you saved this pipeline in your home
-   directory, you can just execute `~/assembly.pbs/RUNME-2.bash` insted from any
-   location in the head node.
-
-2. I executed step 2, and Velvet worked but SOAP failed (or vice versa).  Can I
-   submit only one of them?
-
-   Yes.  To execute only Velvet, run:
-```
-   ./RUNME-2.bash <name> velvet
-```
-
-   To execute only SOAP, run:
-```
-   ./RUNME-2.bash <name> soap
-```
-
-3. I ran step 2, and most of the jobs finished, but few of them failed.  Can I
-   submit only few K-mers?
-
-   Yes.  To execute one kmer (say, the k-mer 33 of SOAP), run:
-```
-   ./RUNME-2.bash <name> soap 33
-```
-
-   You can also execute more than one kmer, using a comma-separated list.  For
-   example, to re-submit the k-mers 37, 39, and 41 of Velvet, run:
-```
-   ./RUNME-2.bash <name> velvet 37,39,41
-```
-
-4. What are the numbers on the job names of step 2?
-
-   The K-mer.  Each k-mer has it's own job, but they are "arrayed", to simplify
-   administration: notice that all the jobs of Velvet and all the jobs of SOAP
-   share the same job ID.
-
-5. Some jobs are being killed, why?
-
-   5.1. First, check the log file created by the pipeline.  The name is typically
-      the output prefix and the .log extension.  For velvet, there are two log files,
-      the `.glog` and the `.hlog`.  You may find the problem there.
-
-   5.2. Now, check the error file in your HOME directory.  The name depends on the
-      job, the library and the task.  For example: `~/soap_Mg_2-37.e1999838` is the
-      error file for step 2, task soap, library Mg_2, k-mer 37.  The appending
-      number after the 'e' is the job ID.  If this file contains errors probably
-      related to the pipeline, please let me know.
-
-   5.3. If you still have no clues, check the output file in your `HOME` directory.  The
-      name is just like the name of the error file (see #5.2 above), but with 'o'
-      instead of 'e'.  Compare the lines 'Resources' (what we asked the scheduler for)
-      and 'Rsrc Used' (what the job actually used).  A typical problem is that your
-      job may need more RAM than we asked for (the value of 'mem' in both lines).  If
-      the RAM used is larger than the RAM requested, the scheduler probably killed
-      your job.  To solve this, just go to your config file, and set the variable
-      RAMMULT to a number larger than 1.  For example, if you want to ask for double the
-      RAM, set `RAMMULT=2`.  You can also include simple arithmetic operations, like
-      `RAMMULT=3/2`.  If you want to add a fixed ammount of RAM, in Gib, use addition.
-      For example, to add 10G, set `RAMMULT=1+10`.
-
-   5.4.  Still no idea?  Try running the job again, sometimes the jobs fail with no
-      apparent reason, but they succeed when re-submited.  If your job keeps failing,
-      please gather as much information (the log, error and output files should be
-      enough) and let me take a look.
-
-6. In the step 2, some k-mers keep failing, and I just want to give up on them, can I?
-   
-   Yes.  Step 3 will analyze only completed jobs, so you can just ignore these faulty
-   k-mers.  Very small k-mers, for example, sometimes need too much memory, and very
-   large k-mers in Velvet sometimes need too much time.  If you don't think you're
-   missing too much, just ignore them.
-

data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash

@@ -1,112 +0,0 @@
-#!/bin/bash
-
-##################### HELP
-HELP="
-Usage:
-   $0 name[ prog[ k-mers]]
-   
-   name		The name of the run.  CONFIG.name.bash must exist.
-   prog		Program to execute.  One of 'soap' or 'velvet'.  By
-   		default, it executes both.
-   k-mers	Comma-separated list of k-mers to run.  By default,
-   		it executes all the odd numbers between 21 and 63
-		(inclusive).
-   
-   See $PDIR/README.txt for more information.
-"
-##################### RUN
-# Find the directory of the pipeline
-PDIR=$(dirname $(readlink -f $0));
-# Load variables
-source "$PDIR/RUNME.bash"
-if [[ "$SCRATCH" == "" ]] ; then
-  echo "$0: Error loading $PDIR/RUNME.bash, variable SCRATCH undefined" >&2
-  exit 1
-fi
-
-# Check request
-RUNVELVET=yes
-RUNSOAP=yes
-if [[ "$2" == "velvet" ]] ; then
-  RUNSOAP=no
-elif [[ "$2" == "soap" ]] ; then
-  RUNVELVET=no
-fi
-if [[ "$3" == "" ]] ; then
-  KMERARRAY="21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63"
-else
-  KMERARRAY=$3
-fi
-if [[ "$VELVETSIM" == "" ]] ; then
-  VELVETSIM=22
-fi
-if [[ "$SOAPSIM" == "" ]] ; then
-  let SOAPSIM=130/$PPN
-fi
-
-# Run it
-RAMMULT=${RAMMULT:-1}
-echo "Jobs being launched in $SCRATCH"
-for LIB in $LIBRARIES; do
-  # Prepare info
-  echo "Running $LIB";
-  if [[ "$USECOUPLED" == "yes" ]] ; then
-    INPUT="$DATA/$LIB.CoupledReads.fa"
-  elif [[ "$USESINGLE" == "yes" ]] ; then
-    INPUT="$DATA/$LIB.SingleReads.fa"
-  else
-    echo "$0: Error: No task selected, neither USECOUPLED nor USESINGLE set to yes." >&2
-    exit 1;
-  fi
-  VARS="LIB=$LIB,PDIR=$PDIR,DATA=$DATA,USECOUPLED=$USECOUPLED,USESINGLE=$USESINGLE"
-  [[ -n $INSLEN ]] && VARS="$VARS,INSLEN=$INSLEN"
-  [[ -n $VELVETG_EXTRA ]] && VARS="$VARS,VELVETG_EXTRA=$VELVETG_EXTRA"
-  [[ -n $VELVETH_EXTRA ]] && VARS="$VARS,VELVETH_EXTRA=$VELVETH_EXTRA"
-  [[ -n $CLEANUP ]] && VARS="$VARS,CLEANUP=$CLEANUP"
-  let SIZE=$(ls -lH "$INPUT" | awk '{print $5}')/1024/1024/1024;
-  let RAMS=40+$SIZE*10*$RAMMULT;
-  let RAMV=50+$SIZE*15*$RAMMULT;
-  # Launch Velvet
-  if [[ "$RUNVELVET" == "yes" ]] ; then
-    NAME="velvet_${LIB}"
-    if [[ "$QUEUE" != "" ]]; then
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l "walltime=$WTIME" -q "$QUEUE" \
-          -t "$KMERARRAY%$VELVETSIM"
-    elif [[ $RAMV -gt 150 ]]; then
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l walltime=360:00:00 -q biohimem-6 \
-          -t "$KMERARRAY%$VELVETSIM"
-    elif [[ $SIZE -lt 6 ]]; then
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l walltime=12:00:00 -q iw-shared-6 \
-          -t "$KMERARRAY%$VELVETSIM"
-    elif [[ $SIZE -lt 20 ]]; then
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l walltime=120:00:00 -q bioforce-6 \
-          -t "$KMERARRAY%$VELVETSIM"
-    else
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l walltime=360:00:00 -q biocluster-6 \
-          -t "$KMERARRAY%$VELVETSIM"
-    fi
-  fi
-  # Launch SOAP
-  if [[ "$RUNSOAP" == "yes" ]] ; then
-    NAME="soap_${LIB}"
-    if [[ "$QUEUE" != "" ]]; then
-      qsub "$PDIR/soap.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMS}gb -l walltime=$WTIME -q $QUEUE -l nodes=1:ppn=$PPN \
-          -t "$KMERARRAY%$SOAPSIM"
-    elif [[ $RAMS -gt 150 ]]; then
-      qsub "$PDIR/soap.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMS}gb -l walltime=48:00:00 -q biohimem-6 \
-          -l nodes=1:ppn=$PPN -t "$KMERARRAY%$SOAPSIM"
-    else
-      qsub "$PDIR/soap.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMS}gb -l walltime=12:00:00 -q iw-shared-6 \
-          -l nodes=1:ppn=$PPN -t "$KMERARRAY%$SOAPSIM"
-    fi
-  fi
-done
-

data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash

@@ -1,23 +0,0 @@
-#!/bin/bash
-
-##################### RUN
-# Find the directory of the pipeline
-PDIR=$(dirname $(readlink -f $0));
-# Load variables
-source "$PDIR/RUNME.bash"
-if [[ "$SCRATCH" == "" ]] ; then
-   echo "$0: Error loading $PDIR/RUNME.bash, variable SCRATCH undefined" >&2
-   exit 1
-fi
-
-# Run it
-echo "Jobs being launched in $SCRATCH"
-for LIB in $LIBRARIES; do
-   # Prepare info
-   echo "Running $LIB";
-   VARS="LIB=$LIB,PDIR=$PDIR"
-   # Launch Stats
-   NAME="N50_${LIB}"
-   qsub "$PDIR/stats.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME"
-done
-