[Patchwork-commits] r181 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork pkg/patchwork/R www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 27 17:17:23 CEST 2013
Author: sebastian_d
Date: 2013-06-27 17:17:23 +0200 (Thu, 27 Jun 2013)
New Revision: 181
Modified:
.git/COMMIT_EDITMSG
.git/index
.git/logs/HEAD
.git/logs/refs/heads/master
.git/logs/refs/remotes/origin/master
.git/refs/heads/master
.git/refs/remotes/origin/master
pkg/patchwork/DESCRIPTION
pkg/patchwork/R/patchwork.plot.r
pkg/patchwork/R/patchwork.readChroms.r
pkg/patchwork/R/patchwork.segment.r
www/TAPS_requ.php
www/changelog.php
www/pw_inst.php
Log:
Update regarding pysam and pysam information on homepage
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2013-06-25 13:00:49 UTC (rev 180)
+++ .git/COMMIT_EDITMSG 2013-06-27 15:17:23 UTC (rev 181)
@@ -1 +1 @@
-added some images that i forgot
+Move pysam out of package
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-06-25 13:00:49 UTC (rev 180)
+++ .git/logs/HEAD 2013-06-27 15:17:23 UTC (rev 181)
@@ -53,3 +53,6 @@
86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076903 +0200 commit: small change to alleledata to fix HG check.
5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 998b2f7c44be9ba4a1a31c630143e4f755bf3b32 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162569 +0200 commit: added some images that i forgot
998b2f7c44be9ba4a1a31c630143e4f755bf3b32 e557c8daaad5d3fba321242275706fa9e3138286 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162589 +0200 pull : Merge made by recursive.
+e557c8daaad5d3fba321242275706fa9e3138286 c8a8af10a9f5c2312766cbebef91ffa9126061e5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372165351 +0200 commit: small fix (hopefully) removing medians that have been set to NA
+c8a8af10a9f5c2312766cbebef91ffa9126061e5 5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372169352 +0200 commit: deleting pysam to upgrade and test newer version
+5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 c08551d489e8bc28692c600dfffa7e7d4cb37ca5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372256038 +0200 commit: Move pysam out of package
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-06-25 13:00:49 UTC (rev 180)
+++ .git/logs/refs/heads/master 2013-06-27 15:17:23 UTC (rev 181)
@@ -53,3 +53,6 @@
86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076903 +0200 commit: small change to alleledata to fix HG check.
5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 998b2f7c44be9ba4a1a31c630143e4f755bf3b32 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162569 +0200 commit: added some images that i forgot
998b2f7c44be9ba4a1a31c630143e4f755bf3b32 e557c8daaad5d3fba321242275706fa9e3138286 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162589 +0200 pull : Merge made by recursive.
+e557c8daaad5d3fba321242275706fa9e3138286 c8a8af10a9f5c2312766cbebef91ffa9126061e5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372165351 +0200 commit: small fix (hopefully) removing medians that have been set to NA
+c8a8af10a9f5c2312766cbebef91ffa9126061e5 5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372169352 +0200 commit: deleting pysam to upgrade and test newer version
+5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 c08551d489e8bc28692c600dfffa7e7d4cb37ca5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372256038 +0200 commit: Move pysam out of package
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-06-25 13:00:49 UTC (rev 180)
+++ .git/logs/refs/remotes/origin/master 2013-06-27 15:17:23 UTC (rev 181)
@@ -51,3 +51,6 @@
86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076931 +0200 update by push
5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 d638a39e4e15a398cf8459744395a830bbd12287 Sebastian DiLorenzo <S_D at imv096.medsci.uu.se> 1372162589 +0200 pull : fast-forward
d638a39e4e15a398cf8459744395a830bbd12287 e557c8daaad5d3fba321242275706fa9e3138286 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162603 +0200 update by push
+e557c8daaad5d3fba321242275706fa9e3138286 c8a8af10a9f5c2312766cbebef91ffa9126061e5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372165363 +0200 update by push
+c8a8af10a9f5c2312766cbebef91ffa9126061e5 5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372169371 +0200 update by push
+5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 c08551d489e8bc28692c600dfffa7e7d4cb37ca5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372256058 +0200 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-06-25 13:00:49 UTC (rev 180)
+++ .git/refs/heads/master 2013-06-27 15:17:23 UTC (rev 181)
@@ -1 +1 @@
-e557c8daaad5d3fba321242275706fa9e3138286
+c08551d489e8bc28692c600dfffa7e7d4cb37ca5
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-06-25 13:00:49 UTC (rev 180)
+++ .git/refs/remotes/origin/master 2013-06-27 15:17:23 UTC (rev 181)
@@ -1 +1 @@
-e557c8daaad5d3fba321242275706fa9e3138286
+c08551d489e8bc28692c600dfffa7e7d4cb37ca5
Modified: pkg/patchwork/DESCRIPTION
===================================================================
--- pkg/patchwork/DESCRIPTION 2013-06-25 13:00:49 UTC (rev 180)
+++ pkg/patchwork/DESCRIPTION 2013-06-27 15:17:23 UTC (rev 181)
@@ -1,11 +1,11 @@
Package: patchwork
Type: Package
Title: Allele-specific Copy Number Analysis of whole genome data
-Version: 2.2
+Version: 2.3
Date: 2012-30-08
Author: Markus Mayrhofer, Sebastian DiLorenzo
Maintainer: Markus Mayrhofer <Markus.Mayrhofer at medsci.uu.se>
Description: Performs a allele-specific copy number analysis of whole genome data.
License: GPL-2
#Imports: patchworkData
-#Depends: DNAcopy
+Suggests: DNAcopy
Modified: pkg/patchwork/R/patchwork.plot.r
===================================================================
--- pkg/patchwork/R/patchwork.plot.r 2013-06-25 13:00:49 UTC (rev 180)
+++ pkg/patchwork/R/patchwork.plot.r 2013-06-27 15:17:23 UTC (rev 181)
@@ -159,7 +159,7 @@
}
#Segment the data.
- library(DNAcopy)
+ #library(DNAcopy)
segs = NULL
try( load(paste(name,"_Segments.Rdata",sep="")), silent=TRUE )
if(length(segs) == 0)
Modified: pkg/patchwork/R/patchwork.readChroms.r
===================================================================
--- pkg/patchwork/R/patchwork.readChroms.r 2013-06-25 13:00:49 UTC (rev 180)
+++ pkg/patchwork/R/patchwork.readChroms.r 2013-06-27 15:17:23 UTC (rev 181)
@@ -26,22 +26,22 @@
system(paste("cp -r ",packagepath,"/python .python",sep=""))
#If import pysam doesnt work, ie pysam isnt installed yet, we install pysam.
- if (system(paste("python ",getwd(),"/.python/Check.py",sep=""),intern=T) == "Pysam Not Available")
- {
- setwd(".python")
- cat("Pysam has not yet been installed on your system. \n Attempting to Build \n")
- system("sleep 5")
- # build pysam
- system("python setup.py build > pysam_build_output.txt")
- system("cp pysam_build_output.txt ..")
- cat("Build complete. Output of build can be viewed in file pysam_build_output.txt.
- \n Attempting to Install \n")
- # install pysam to site.USER_BASE
- system("python setup.py install --user > pysam_install_output.txt")
- system("cp pysam_install_output.txt ..")
- cat("Install complete. Output of install can be viewed in file pysam_install_output.txt. \n")
- setwd("..")
- }
+ # if (system(paste("python ",getwd(),"/.python/Check.py",sep=""),intern=T) == "Pysam Not Available")
+ # {
+ # setwd(".python")
+ # cat("Pysam has not yet been installed on your system. \n Attempting to Build \n")
+ # system("sleep 5")
+ # # build pysam
+ # system("python setup.py build > pysam_build_output.txt")
+ # system("cp pysam_build_output.txt ..")
+ # cat("Build complete. Output of build can be viewed in file pysam_build_output.txt.
+ # \n Attempting to Install \n")
+ # # install pysam to site.USER_BASE
+ # system("python setup.py install --user > pysam_install_output.txt")
+ # system("cp pysam_install_output.txt ..")
+ # cat("Install complete. Output of install can be viewed in file pysam_install_output.txt. \n")
+ # setwd("..")
+ # }
readlength=80 # this is currently hard coded and may be adjusted.
seglength=200 # (do not change)
Modified: pkg/patchwork/R/patchwork.segment.r
===================================================================
--- pkg/patchwork/R/patchwork.segment.r 2013-06-25 13:00:49 UTC (rev 180)
+++ pkg/patchwork/R/patchwork.segment.r 2013-06-27 15:17:23 UTC (rev 181)
@@ -1,6 +1,6 @@
patchwork.segment <- function(kbsegs,chroms,Alpha,SD)
{
- #library(DNAcopy)
+ library(DNAcopy)
#Load data included in package
#packagepath = system.file(package="patchwork")
#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
Modified: www/TAPS_requ.php
===================================================================
--- www/TAPS_requ.php 2013-06-25 13:00:49 UTC (rev 180)
+++ www/TAPS_requ.php 2013-06-27 15:17:23 UTC (rev 181)
@@ -13,8 +13,8 @@
Using Nexus has the benefit of being able to use their segmentation which reduces running time of TAPS.
<br /><br />
-If you have used <b>Nexus</b>, locate the samples folder, which is what TAPS takes as input. It should
-contain the files "probes.txt", "snps.txt" and "segments.txt".
+If you have used <b>Nexus</b>, use "File -> Utilities -> Export from .ivg to.txt" to create "probes.txt",
+ "snps.txt" and "segments.txt". These should be in a sample folder, which is what TAPS takes as input.
<br /><br />
If you have used <b>ChAS</b>, load the file ending in "cyhd.cychp" into ChAS and create the text file ending in "cyhd.txt"
Modified: www/changelog.php
===================================================================
--- www/changelog.php 2013-06-25 13:00:49 UTC (rev 180)
+++ www/changelog.php 2013-06-27 15:17:23 UTC (rev 181)
@@ -10,11 +10,19 @@
<h5 style="display:inline-block;">patchwork v2.3 - </h5><div style="display:inline-block; width:1px;"></div>
<h6 style="display:inline-block;">2013</h6>
<ul>
- <li>Update the version of Pysam that Patchwork uses for general compatibility</li>
- fixes to mpileup reading
- improvements in all the plots for patchwork, including cytoband information
+ <li>Moved Pysam out of package due to auto-install issues. Now you will have to manually install it.
+ See Patchwork -> Installation </li>
</ul> -->
+ <hr class="alt1" />
+
+<h5 style="display:inline-block;">patchwork v2.3 - </h5><div style="display:inline-block; width:1px;"></div>
+<h6 style="display:inline-block;">2013</h6>
+<ul>
+ <li>Moved Pysam out of package due to auto-install issues. Now you will have to manually install it.
+ See Patchwork -> Installation </li>
+</ul>
+
<hr class="alt1" />
<h5 style="display:inline-block;">patchwork / TAPS - </h5><div style="display:inline-block; width:1px;"></div>
Modified: www/pw_inst.php
===================================================================
--- www/pw_inst.php 2013-06-25 13:00:49 UTC (rev 180)
+++ www/pw_inst.php 2013-06-27 15:17:23 UTC (rev 181)
@@ -45,10 +45,15 @@
<h4>Python and Pysam</h4>
-Patchwork uses a python mod called pysam for "reading" the chromosomes. The package already checks if you have
+<!-- Patchwork uses a python mod called pysam for "reading" the chromosomes. The package already checks if you have
it installed and otherwise installs it for you the first time you run patchwork however if you lack python
or python development on your system the installation fails. It seems to already be included in MAC OS X but
on other systems you should install/update it. Here is a
<a href="http://wiki.python.org/moin/BeginnersGuide/Download" target="_blank" style="text-decoration:none;">guide.</a>
-<br />
-
\ No newline at end of file
+<br /> -->
+
+Patchwork uses a python mod called pysam for "reading" the chromosomes. <br /> Currently
+<a href="https://code.google.com/p/pysam" target="_blank" style="text-decoration:none;">Pysam 0.7.4</a>
+and
+<a href="http://www.python.org/download/releases/2.6.7/" target="_blank" style="text-decoration:none;">Python 2.6.7 and 2.7.1</a>
+are tested and supported.
More information about the Patchwork-commits
mailing list