From 09fa3f0bf17a7e6ad966632bce6eca34e4bf2fc3 Mon Sep 17 00:00:00 2001 From: Kelly Vincent Date: Wed, 24 Feb 2010 07:11:43 -0500 Subject: [PATCH] Updated Bowtie test files to handle new version (0.12.3) of Bowtie (bowtie_color_wrapper will fail until new version installed). Updated samtools tools test files. Removed version references from Bowtie and BWA tools. --- test-data/sam_to_bam_out1.bam | Bin 3592 -> 0 bytes tools/samtools/sam_merge.xml | 2 +- tools/samtools/sam_pileup.xml | 2 +- tools/samtools/sam_to_bam.xml | 2 +- tools/sr_mapping/bowtie_color_wrapper.xml | 30 ++++++++++------------ tools/sr_mapping/bowtie_wrapper.xml | 30 ++++++++++------------ tools/sr_mapping/bwa_wrapper.xml | 2 -- 7 files changed, 31 insertions(+), 37 deletions(-) delete mode 100644 test-data/sam_to_bam_out1.bam diff --git a/test-data/sam_to_bam_out1.bam b/test-data/sam_to_bam_out1.bam deleted file mode 100644 index 95c65de857205099e47815d35fa2ae4861d9fba4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3592 zcmV+j4)^gNiwFb&00000{{{d;LjnNn4V_v|Z)8^y^{`+OkVrQp;UGk4kE1-0&`gi# z(+fmR1y!<`fJ8||*+h;PW`~4&!PeFwc}14|1y=ks7KvEQ4(>hY)a&~u3C!3tw)^AV zck9;2Ij5@q%%0ymXkY(m-`{QDzdHZppP%;^4o=#4q-A=hdAeJgnOpxI(O!&bFSf_+ zNB?S9TI9Uc`_4?;UBLY{z;1-?zu03)+C`_I9sAr)gBKV18_Kb$db4-6k)94ul z#_&vAb~|yPV5%)V%#!Lqd!-m`Le>~E3y#OTO5=rx8MQ!6X(FslW~8M&hQb}|HMI>R z+ieTPiTicSok2h@+oEz&XJ@^bH}wn+ zc(Er@HxM3UIk{R)6g zxPQpuKoAuogaCQvbg`>W8FCvT97xJ~1HSi%fbxz-EY}{~o^LG%-NkzkpEch$SDq_0 z{rOoU-OH(95B^^QOp;%ajm|xzkdrCZPuZ_=*5k-I@CZysN`Wwp@)H!;Elos092U`kFED#*`0t}u`2m^6)vy3b(- zrug1@Hc>_C1Vr1#FT+`J#1!B$MgWGScRlI7Y`J#PQ*VzFyI%k2t)zQ8o}to=oEcvF z0o4&f_8b$DzEIt$EFp-L9RxHKosAG4uE4@2uEj+`#9}9Nko5+X=!IW#0g5tj;JR+2 zIEUhDL6QbhRz3zn(xF6kZW(+Rb-PH3R7vO|6Be$uG6e3Dt4F$GSqe)OykN&a*0=8g}=MVutqeNOYe~Zc??olhNuZW=XMskEOkp(y!jCO^pRQzCqSb;HHOi}a# zU<#6gy`458Ig)Xe$&AiEC2)pdX0wkgn(gE)ex}^yi(_29BoiW;w49ktg%Io`jF>Q_ zKYZi0vIhgZOR6cmQk})I^5D-yiGXcW1dZbMva=%qR_rUko-N^J35CHC;-Bmj}13zAH_ke$GT8@6_;B| z@A=4dQBwd@(4`InXi>wG;DI}B4v8o{U_Yn<2HQzuKOi1t$nJ8162;x<&VuqyL1p)e zl%cy`(f$P$J&fTrW((vEQh$7WT(_1=N|N1at4-kIae+lvpPn22{o!`gsE>#VZoFcs5!j2 zksXjmksLJyPs*~D;}`WBIWv??97&X@Ib*lOR~9G%VN|ojIru@D<&_{PsK|ws28|;y z1yEG*gdA|ztfBfvgPTkmL+z7D71IeqlGJ&SSQc%Ay5gK?o<1Y5#x}vxmA#^1yu`0m z7x0i|N?y&Hj3Sv9lOL;D#N05TR_6MyKFcK#1`l^2%aYkOhf8gvX&=MGj2w3jA#cqP z#I+&#FPb#f)uQOiJX5OWzMUnHsc9!M4Z&gHT)dVX&q5P1MR*RchHv240;V~1^iC8c z*32Wd#}Z66vZ>al)T<84TZh+KMuXX8l-#q@;ie==NS4EH-f2KHEiSzpXY5^sBFw`sPn;KW|44D{kV%{ops9y1{aT& zBh=J1wHSJ#isml%l_oT6=2NXQI|VOaN&bf>42wi`j6NLsoAVr}x@ApEL+#*_bJW5( zb(0XMyGpQv?FoqfwFvZH^>NF1R+n(9 z9fD3q)nsTUAwU>+b$E6q=DP(`UG`8U!c=i{N-@I7K|BYEi1NGLV`wXaQ@X0fJXc zraOsrC8SdYJmxUxOVBwr3S&a2WQk@4PR<;$2{{|3C9Nh?G5eg%gQugLYE(G)(`Bzy z=MnNk;I<%1uQ^<3zQ)hgJZi|G23`ZcC0%*xSM^U>pG@v2#w=qFX%^zgeO@3Am}`jH zXd)5h&Vc@81hW#Y!Q!tWn|m>qW_=5i+?S4feSlMw4b!K0HV+@hF}iESUR)z351Td1 z5kVu*UlH)d?1dpdQ@HXoDN+Hn`&|POhYnN8FgfHkR8?dZkNeVK6VKHrF)2@JKw&j= zuw}=g&y}Rytr`TO<2><|gBL^I{Wuw;qoMyy0($lGUf~-dJk;6pz54Vg_{lVtvC5%OCdK+u&D0M7rTZCIg1#*KD=kMPpzc^ zs4YY-Wj-@O-9k_!a(tuubBWF|hl%pg3#kkd6Vu-`o}| zFk+KNjpCP@l@VoJnyDoIVvNp?FG{Hh$ysByo2#36B_&W=Q4_e5lRzrAx}sT8=VC&j zO(dsXIwFN|Rv&JKROn(<1=o6J?9YSNH&_^v1*EL35r^kaM#G-mi#IY*!5kw$;4p#_ z1+#2bIhACugGiVB8o@N?k7FoKtuAE1*acJjX>__@>JobVY`la!GaWfxjzr}}j4Hfx zE!04|&m*9$*^1|^T*r@sLY~o|dL;k2s3Md6blx(m0~nU-^bA9Bbol-VfSO3XyWjPE zcd@(ZA1%K2?|JE)E$hF(VOMZ;@g>qOrG({4&EJOLxD6QY^#@T!In|rGrW!ep(XBkM zze6gtXOg8xL;G<6mVWPmGgB_aOJB6_|Fo}vzIAYL=bew%w+`MuIM!?Zt6%fsA3pl! zZ|wI^x1Vi4JGuAx$rH0rJ~`d?e~+F%IeoZ&bnxr%92{IFZy&Zt20t&;8aXTfg=EgHIoSeDCA?k7tv9_k$ambka) z4_AjrM_;_0uGZM|CqG*nvw2;U{{Evf>EKOFdc1vf`e1tklk95q?pN2BSF6p@<@IFO z)77gU`KGULH|ej(H!|tb$%E7T+bvDHz4`6Grx%Co7wh%)@s%B4{vVTCSns^|?IwNt z-i-qHaC>t4c>540O*XAJoAu>tb9MRR?w708dV1^o)AZBn&dqXZ_5RIrX?ySV=~H@X zI=XyubZNKkaCJGo`{i_aHNCT%j;D8~GU|tKWYS-Lej}3}Z?~uSA3TLg>&t|E@ zzWwa(%k}lq|45F9dBS>OHYcsgn}ygyApzM+%;_2@=Uy1#wW zJjGO6uU1oo$JOd^wVCdIdDyeNZ~FEdn)F{EsySUOEC2u>iwFb&00000{{{d;LjnLB O00RI3000000001Z^!VBU diff --git a/tools/samtools/sam_merge.xml b/tools/samtools/sam_merge.xml index b18dd681291..a0aeab23dbf 100644 --- a/tools/samtools/sam_merge.xml +++ b/tools/samtools/sam_merge.xml @@ -1,4 +1,4 @@ - + merges BAM files together sam_merge.py diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml index f2a8362f215..be296f2b525 100644 --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -1,4 +1,4 @@ - + from BAM dataset sam_pileup.py diff --git a/tools/samtools/sam_to_bam.xml b/tools/samtools/sam_to_bam.xml index 024b880e2dd..1bdbcd61ae0 100644 --- a/tools/samtools/sam_to_bam.xml +++ b/tools/samtools/sam_to_bam.xml @@ -1,4 +1,4 @@ - + converts SAM format to BAM format sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml index 5974f41bf2b..b515e5072e6 100644 --- a/tools/sr_mapping/bowtie_color_wrapper.xml +++ b/tools/sr_mapping/bowtie_color_wrapper.xml @@ -197,12 +197,12 @@ - - - - - - + + + + + + @@ -252,7 +252,7 @@ - + @@ -262,9 +262,9 @@ - - - + + + @@ -327,9 +327,9 @@ - - - + + + @@ -417,7 +417,7 @@ @@ -533,8 +533,6 @@ Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. -This tool uses Bowtie version 0.12.1. - .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml ------ diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml index d2c23e6f0f1..eb3bb78c737 100644 --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -191,13 +191,13 @@ - - - - - - - + + + + + + + @@ -246,7 +246,7 @@ - + @@ -256,9 +256,9 @@ - - - + + + @@ -315,9 +315,9 @@ - - - + + + @@ -506,8 +506,6 @@ Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. -This tool uses Bowtie version 0.12.1. - .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml ------ diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml index d90e34916de..20cba4a5066 100644 --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -181,8 +181,6 @@ BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60. -This tool uses BWA version 0.5.5. - ------ **Know what you are doing**