error with install AmpliconNoise

[yings...@126.com]

I have installed gsl-1.9 and openmpi-1.6.4

when i install  AmpliconNoise, type make:

Perseus.c:14:24: error: gsl/gsl_sf.h: No such file or directory
Perseus.c:15:29: error: gsl/gsl_randist.h: No such file or directory
make[1]: *** [Perseus.o] Error 1
make: *** [all] Error 2

when i type mpicc --version, i have output

but type gsl --version, it bash

so I think maybe i install the gsl incorrectly, i install qiime in suse linux which is public server , so i can't install in default ,need to my directory

that's my doing:

tar –zxvf gsl-1.9.tar.gz.tar.gz.tar.gz

cd gsl-1.9

./configure --prefix=$HOME/qiime-software/gsl-1.9

make

make install

make clean

echo "export PATH=$HOME/qiime-software/ gsl-1.9/bin/:$PATH" >> $HOME/.bashrc

source $HOME/.bashrc

would you like to help checking what's the problem?

[Will Van Treuren]

Hi,

It does seem that gsl is improperly installed. Have you tried installing the gsl-dev package (either gsl-devel or gsl-dev)? 

Are you experiencing any errors with the QIIME installation or just with gsl?

Thanks,

Will 

--
 
---
You received this message because you are subscribed to the Google Groups "Qiime Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to qiime-forum...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[yings...@126.com]

i haven't tried gsl package, because in another computer of fedora linux , the gsl-1.9 is ok, but in that computer i install it in default directory.

as you say, i may try the gsl-dev package.

i try installl QIIME-1.7 as http://qiime.org/install/install.html by steps. now i step in ampliconnoise. until now, i only have the problem with pplacer of unsupported version, but i download it from http://matsen.fhcrc.org/pplacer/builds/pplacer-v1.1-Linux.tar.gz, i think it is right.

because i  install it step by step, of course i don't have install some dependencies , which are

• ghc 6.8 (required by the QIIME denoiser) (src_ghc)

Visualization and plotting steps:

• MatPlotLib 1.1.0 (src_matplotlib) (license: PFS)
• cytoscape v2.7.0 (src_cytoscape) (license: LGPL)

Supervised learning (supervised_learning.py) and compare_categories.py:

• R 2.12.0 (src_r) See R install notes. (license: GPL2)

Assigning taxonomy using BLAST or picking OTUs against Greengenes filtered at 97% identity:

• Greengenes OTUs, taxonomies, and trees (.tar.gz)

If you plan to build the QIIME documentation locally:

• Sphinx 1.0.4 (src) See Building the QIIME documentation (license: BSD)

If you plan to use remote mapping files (stored as Google Spreadsheets) with QIIME (see the tutorial here):

• gdata 2.0.17 (src) (license: Apache 2.0)

If you plan to use SourceTracker with QIIME:

• SourceTracker 0.9.5 (src) (license: GPL)

在 2013年6月10日星期一UTC+8上午3时41分48秒，Will Van Treuren写道：

[yings...@126.com]

i tried install the gsl-1.15, still got the same error.

在 2013年6月10日星期一UTC+8上午3时41分48秒，Will Van Treuren写道：

Hi,

[Will Van Treuren]

Hi, 

Can you post the output of print_qiime_config.py -t?

Thanks,

Will 

[yings...@126.com]

i'm sorry so late to post because of some exams

this is the output without install the ampliconnoise

quanzx@compile:~> print_qiime_config.py -t

System information

==================

         Platform:      linux2

   Python version:      2.7.3 (default, Jun  8 2013, 18:28:18)  [GCC 4.1.2 20070115 (SUSE Linux)]

Python executable:      /home/users/quanzx/qiime-software/Python-2.7.3/bin/python2.7

Dependency versions

===================

                     PyCogent version:  1.5.3

                        NumPy version:  1.5.1

                   matplotlib version:  Not installed.

                  biom-format version:  1.1.2

                QIIME library version:  1.7.0

                 QIIME script version:  1.7.0

        PyNAST version (if installed):  1.2

RDP Classifier version (if installed):  rdp_classifier-2.2.jar

          Java version (if installed):  1.7.0_21

QIIME config values

===================

                     blastmat_dir:      None

                         sc_queue:      all.q

      topiaryexplorer_project_dir:      None

     pynast_template_alignment_fp:      /home/users/quanzx/qiime-software/core_set_aligned.fasta.imputed

                  cluster_jobs_fp:      None

pynast_template_alignment_blastdb:      None

assign_taxonomy_reference_seqs_fp:      /home/users/quanzx/qiime-software/gg_12_10_otus/rep_set/97_otus.fasta

                     torque_queue:      friendlyq

   template_alignment_lanemask_fp:      /home/users/quanzx/qiime-software/lanemask_in_1s_and_0s.txt

                    jobs_to_start:      1

                cloud_environment:      False

                qiime_scripts_dir:      /home/users/quanzx/qiime-software/bin/

            denoiser_min_per_core:      50

                      working_dir:      None

                    python_exe_fp:      python

                         temp_dir:      /tmp/

                      blastall_fp:      blastall

                 seconds_to_sleep:      2

assign_taxonomy_id_to_taxonomy_fp:      /home/users/quanzx/qiime-software/gg_12_10_otus/taxonomy/97_otu_taxonomy.txt

running checks:

test_FastTree_supported_version (__main__.Qiime_config)

FastTree is in path and version is supported ... ok

test_INFERNAL_supported_version (__main__.Qiime_config)

INFERNAL is in path and version is supported ... ok

test_ParsInsert_supported_version (__main__.Qiime_config)

ParsInsert is in path and version is supported ... ok

test_R_supported_version (__main__.Qiime_config)

R is in path and version is supported ... FAIL

test_ampliconnoise_install (__main__.Qiime_config)

AmpliconNoise install looks sane. ... FAIL

test_blast_supported_version (__main__.Qiime_config)

blast is in path and version is supported ... ok

test_blastall_fp (__main__.Qiime_config)

blastall_fp is set to a valid path ... ok

test_blastmat_dir (__main__.Qiime_config)

blastmat_dir is set to a valid path. ... ok

test_cdbtools_supported_version (__main__.Qiime_config)

cdbtools is in path and version is supported ... ok

test_cdhit_supported_version (__main__.Qiime_config)

cd-hit is in path and version is supported ... ok

test_chimeraSlayer_install (__main__.Qiime_config)

no obvious problems with ChimeraSlayer install ... ok

test_clearcut_supported_version (__main__.Qiime_config)

clearcut is in path and version is supported ... ok

test_cluster_jobs_fp (__main__.Qiime_config)

cluster_jobs_fp is set to a valid path and is executable ... FAIL

test_denoiser_supported_version (__main__.Qiime_config)

denoiser aligner is ready to use ... FAIL

test_for_obsolete_values (__main__.Qiime_config)

local qiime_config has no extra params ... ok

test_gdata_install (__main__.Qiime_config)

gdata is installed ... ok

test_matplotlib_suported_version (__main__.Qiime_config)

maptplotlib version is supported ... FAIL

test_mothur_supported_version (__main__.Qiime_config)

mothur is in path and version is supported ... ok

test_muscle_supported_version (__main__.Qiime_config)

muscle is in path and version is supported ... ok

test_numpy_suported_version (__main__.Qiime_config)

numpy version is supported ... ok

test_pplacer_supported_version (__main__.Qiime_config)

pplacer is in path and version is supported ... FATAL: kernel too old

FAIL

test_pynast_suported_version (__main__.Qiime_config)

pynast version is supported ... ok

test_pynast_template_alignment_blastdb_fp (__main__.Qiime_config)

pynast_template_alignment_blastdb, if set, is set to a valid path ... ok

test_pynast_template_alignment_fp (__main__.Qiime_config)

pynast_template_alignment, if set, is set to a valid path ... ok

test_python_exe_fp (__main__.Qiime_config)

python_exe_fp is set to a working python env ... ok

test_python_supported_version (__main__.Qiime_config)

python is in path and version is supported ... ok

test_qiime_scripts_dir (__main__.Qiime_config)

qiime_scripts_dir, if set, is set to a valid path ... ok

test_raxmlHPC_supported_version (__main__.Qiime_config)

raxmlHPC is in path and version is supported ... ok

test_rtax_supported_version (__main__.Qiime_config)

rtax is in path and version is supported ... ok

test_sourcetracker_installed (__main__.Qiime_config)

sourcetracker is installed ... FAIL

test_temp_dir (__main__.Qiime_config)

temp_dir, if set, is set to a valid path ... ok

test_template_alignment_lanemask_fp (__main__.Qiime_config)

template_alignment_lanemask, if set, is set to a valid path ... ok

test_uclust_supported_version (__main__.Qiime_config)

uclust is in path and version is supported ... ok

test_usearch_supported_version (__main__.Qiime_config)

usearch is in path and version is supported ... ok

test_working_dir (__main__.Qiime_config)

working_dir, if set, is set to a valid path ... ok

======================================================================

FAIL: test_R_supported_version (__main__.Qiime_config)

R is in path and version is supported

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/users/quanzx/qiime-software/bin/print_qiime_config.py", line 699,in test_R_supported_version

    "which components of QIIME you plan to use.")

AssertionError: R not found. This may or may not be a problem depending on which components of QIIME you plan to use.

======================================================================

FAIL: test_ampliconnoise_install (__main__.Qiime_config)

AmpliconNoise install looks sane.

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/users/quanzx/qiime-software/bin/print_qiime_config.py", line 144,in test_ampliconnoise_install

    "$PYRO_LOOKUP_FILE variable is not set. See %s for help." % url) 

AssertionError: $PYRO_LOOKUP_FILE variable is not set. See http://qiime.org/install/install.html#ampliconnoise-install-notes for help.

======================================================================

FAIL: test_cluster_jobs_fp (__main__.Qiime_config)

cluster_jobs_fp is set to a valid path and is executable

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/users/quanzx/qiime-software/bin/print_qiime_config.py", line 103,in test_cluster_jobs_fp

    self.fail("Your qiime_config file doesn't have cluster_jobs_fp\n.")

AssertionError: Your qiime_config file doesn't have cluster_jobs_fp

.

======================================================================

FAIL: test_denoiser_supported_version (__main__.Qiime_config)

denoiser aligner is ready to use

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/users/quanzx/qiime-software/bin/print_qiime_config.py", line 542,in test_denoiser_supported_version

    "which components of QIIME you plan to use.")

AssertionError: Denoiser flowgram aligner not found or not executable.This may or may not be a problem depending on which components of QIIME you plan to use.

======================================================================

FAIL: test_matplotlib_suported_version (__main__.Qiime_config)

maptplotlib version is supported

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/users/quanzx/qiime-software/bin/print_qiime_config.py", line 377,in test_matplotlib_suported_version

    version_string))

AssertionError: Unsupported matplotlib version. Must be >= 1.1.0 and <= 1.1.0 ,but running Not installed.

======================================================================

FAIL: test_pplacer_supported_version (__main__.Qiime_config)

pplacer is in path and version is supported

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/users/quanzx/qiime-software/bin/print_qiime_config.py", line 647,in test_pplacer_supported_version

    % ('.'.join(map(str,acceptable_version)), version_string))

AssertionError: Unsupported pplacer version. (1, 1).(1, 1) is required, but running .

======================================================================

FAIL: test_sourcetracker_installed (__main__.Qiime_config)

sourcetracker is installed

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/users/quanzx/qiime-software/bin/print_qiime_config.py", line 245,in test_sourcetracker_installed

    ("SOURCETRACKER_PATH is not set. This is "

  File "/home/users/quanzx/qiime-software/Python-2.7.3/lib/python2.7/site-packages/cogent/util/unit_test.py", line 332, in failIfEqual

    % (`observed`, `expected`))

AssertionError: SOURCETRACKER_PATH is not set. This is only important if you plan to use SourceTracker.

----------------------------------------------------------------------

Ran 35 tests in 0.526s

FAILED (failures=7)

在 2013年6月11日星期二UTC+8上午3时53分20秒，Will Van Treuren写道：

[Will Van Treuren]

Hi, 

Can you post the output of the command:

env

I suspect whats wrong is that you don't have either of the following environment variables set:

PYRO_LOOKUP_FILE

SEQ_LOOKUP_FILE

If you don't see either of these variables in the output of the 'env' command, then you need to add them to your bash profile. For instance in my bash profile I have the following lines:

PYRO_LOOKUP_FILE="/Users/wdwvt1/src/AmpliconNoiseV1.27/Data/LookUp_E123.dat"

export PYRO_LOOKUP_FILE

SEQ_LOOKUP_FILE="/Users/wdwvt1/src/AmpliconNoiseV1.27/Data/Tran.dat"

export SEQ_LOOKUP_FILE

See if you can find the location of the corresponding files and put them in your .bashrc file. Hopefully that will resolve the problem.

Best,

Will 

[yings...@126.com]

if i don't care the installing erro, finish the install, and set  the enviroment variables

the output like that:

======================================================================

FAIL: test_ampliconnoise_install (__main__.Qiime_config)

AmpliconNoise install looks sane.

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/users/quanzx/qiime-software/bin/print_qiime_config.py", line 167, in test_ampliconnoise_install

    " See %s for help." % url)

AssertionError: Couldn't find Perseus. Perhaps the AmpliconNoise bin directory isn't in $PATH? See http://qiime.org/install/install.html#ampliconnoise-install-notes for help.

======================================================================

and the command env:

quanzx@compile:~/qiime-software/AmpliconNoiseV1.27> env

MKLROOT=/opt/software/compiler/intel/11.1/072/mkl

LESSKEY=/etc/lesskey.bin

NNTPSERVER=news

INFODIR=/usr/local/info:/usr/share/info:/usr/info

MANPATH=/opt/software/compiler/openmpi/1.4.3/icc.ifort/share/man:/opt/software/compiler/intel/11.1/072/mkl/man/en_US:/opt/software/compiler/intel/11.1/072/man/en_US:/opt/software/compiler/intel/11.1/072/man/en_US:/opt/gridview/pbs//dispatcher//man:/usr/local/man:/usr/local/share/man:/usr/share/man:/usr/X11R6/man:/opt/gnome/share/man

HOSTNAME=node4

GNOME2_PATH=/usr/local:/opt/gnome:/usr

XKEYSYMDB=/usr/X11R6/lib/X11/XKeysymDB

INTEL_LICENSE_FILE=/opt/software/compiler/intel/11.1/072/licenses:/opt/intel/licenses:/home/users/quanzx/intel/licenses:/opt/software/compiler/intel/11.1/072/licenses:/opt/intel/licenses:/home/users/quanzx/intel/licenses

HOST=node4

TERM=xterm

SHELL=/bin/bash

PROFILEREAD=true

HISTSIZE=1000

SSH_CLIENT=11.12.100.1 52879 22

LIBRARY_PATH=/opt/software/compiler/intel/11.1/072/mkl/lib/em64t:/opt/software/compiler/intel/11.1/072/lib/intel64:/opt/software/compiler/intel/11.1/072/lib/intel64

FPATH=/opt/software/compiler/intel/11.1/072/mkl/include

MORE=-sl

OLDPWD=/home/users/quanzx/qiime-software

SSH_TTY=/dev/pts/5

GROFF_NO_SGR=yes

USER=quanzx

PYRO_LOOKUP_FILE=/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/Data/LookUp_E123.dat

LS_COLORS=no=00:fi=00:di=01;34:ln=00;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=41;33;01:ex=00;32:*.cmd=00;32:*.exe=01;32:*.com=01;32:*.bat=01;32:*.btm=01;32:*.dll=01;32:*.tar=00;31:*.tbz=00;31:*.tgz=00;31:*.rpm=00;31:*.deb=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.zip=00;31:*.zoo=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.tb2=00;31:*.tz2=00;31:*.tbz2=00;31:*.avi=01;35:*.bmp=01;35:*.fli=01;35:*.gif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mng=01;35:*.mov=01;35:*.mpg=01;35:*.pcx=01;35:*.pbm=01;35:*.pgm=01;35:*.png=01;35:*.ppm=01;35:*.tga=01;35:*.tif=01;35:*.xbm=01;35:*.xpm=01;35:*.dl=01;35:*.gl=01;35:*.wmv=01;35:*.aiff=00;32:*.au=00;32:*.mid=00;32:*.mp3=00;32:*.ogg=00;32:*.voc=00;32:*.wav=00;32:

LD_LIBRARY_PATH=/opt/software/compiler/openmpi/1.4.3/icc.ifort/lib:/opt/software/compiler/intel/11.1/072/mkl/lib/em64t:/opt/software/compiler/intel/11.1/072/lib/intel64:/opt/software/compiler/intel/11.1/072/lib/intel64:/opt/gridview/pbs//dispatcher//lib::/usr/local/lib64:/usr/local/lib

XNLSPATH=/usr/X11R6/lib/X11/nls

ENV=/etc/bash.bashrc

CPATH=/opt/software/compiler/intel/11.1/072/mkl/include

HOSTTYPE=x86_64

FROM_HEADER=

PAGER=less

CSHEDIT=emacs

XDG_CONFIG_DIRS=/usr/local/etc/xdg/:/etc/xdg/:/etc/opt/gnome/xdg/

NLSPATH=/opt/software/compiler/intel/11.1/072/mkl/lib/em64t/locale/%l_%t/%N:/opt/software/compiler/intel/11.1/072/lib/intel64/locale/%l_%t/%N:/opt/software/compiler/intel/11.1/072/lib/intel64/locale/%l_%t/%N

MINICOM=-c on

MAIL=/var/mail/quanzx

PATH=/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/Scripts:/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/bin:/home/users/quanzx/qiime-software/openmpi-1.6.4/bin/:/home/users/quanzx/qiime-software/gsl-1.9/bin/:/home/users/quanzx/qiime-software/usearch/:/home/users/quanzx/qiime-software/ParsInsert-1.04/:/home/users/quanzx/qiime-software/pplacer-v1.1.alpha14-Linux-3.2.0/:/home/users/quanzx/qiime-software/rtax-0.983/:/home/users/quanzx/qiime-software/muscle/:/home/users/quanzx/qiime-software/cdbfasta/:/home/users/quanzx/qiime-software/infernal-1.0.2/bin/:/home/users/quanzx/qiime-software/infernal-1.0.2/:/home/users/quanzx/qiime-software/infernal-1.0.2/:/home/users/quanzx/qiime-software/infernal-1.0.2/:/home/users/quanzx/qiime-software/infernal-1.0.2/:/home/users/quanzx/qiime-software/infernal/:/home/users/quanzx/qiime-software/stamatak-standard-RAxML-5_7_2012/:/home/users/quanzx/qiime-software/stamatak-standard-RAxML-5_7_2012/:/home/users/quanzx/qiime-software/clearcut/:/home/users/quanzx/qiime-software/readline-master/lib/:/home/users/quanzx/qiime-software/readline-master/:/home/users/quanzx/qiime-software/mothur/Mothur.source/:/home/users/quanzx/qiime-software/Mothur.source/:/home/users/quanzx/qiime-software/microbiomeutil-r20110519/ChimeraSlayer/:/home/users/quanzx/qiime-software/cd-hit/:/home/users/quanzx/qiime-software/blast-2.2.22/bin/:/home/users/quanzx/qiime-software/jdk1.7.0_21/bin/:/home/users/quanzx/qiime-software/FastTree-2.1.3/:/home/users/quanzx/qiime-software/uclust-1.2.22q/:/home/users/quanzx/qiime-software/bin/:/home/users/quanzx/qiime-software/numpy-1.5.1/:/home/users/quanzx/qiime-software/Python-2.7.3/:/home/public/software/blast-2.2.26/bin:/home/users/quanzx/bin/ncbi-blast-2.2.26+/bin:/home/public/software/blast-2.2.26/bin:/home/users/quanzx/bin/ncbi-blast-2.2.26+/bin:/opt/software/compiler/openmpi/1.4.3/icc.ifort/bin:/opt/software/compiler/intel/11.1/072/bin/intel64:/opt/software/compiler/intel/11.1/072/bin/intel64:/opt/gridview/pbs//dispatcher-sched//bin:/opt/gridview/pbs//dispatcher-sched//sbin:/opt/gridview/pbs//dispatcher//bin:/opt/gridview/pbs//dispatcher//sbin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin

CPU=x86_64

SSH_SENDS_LOCALE=yes

INPUTRC=/home/users/quanzx/.inputrc

PWD=/home/users/quanzx/qiime-software/AmpliconNoiseV1.27

LANG=en_US.UTF-8

PYTHONSTARTUP=/etc/pythonstart

TEXINPUTS=:/home/users/quanzx/.TeX:/usr/share/doc/.TeX:/usr/doc/.TeX

QT_SYSTEM_DIR=/usr/share/desktop-data

SHLVL=1

HOME=/home/users/quanzx

LESS_ADVANCED_PREPROCESSOR=no

OSTYPE=linux

LS_OPTIONS=-N --color=tty -T 0

XCURSOR_THEME=Industrial

WINDOWMANAGER=/usr/X11R6/bin/gnome

GTK_PATH=/usr/local/lib/gtk-2.0:/opt/gnome/lib/gtk-2.0:/usr/lib/gtk-2.0

PYTHONPATH=/home/users/quanzx/qiime-software/lib/:

G_FILENAME_ENCODING=@locale,UTF-8,ISO-8859-15,CP1252

LESS=-M -I

MACHTYPE=x86_64-suse-linux

LOGNAME=quanzx

GTK_PATH64=/usr/local/lib64/gtk-2.0:/opt/gnome/lib64/gtk-2.0:/usr/lib64/gtk-2.0

CVS_RSH=ssh

XDG_DATA_DIRS=/usr/local/share/:/usr/share/:/etc/opt/kde3/share/:/opt/kde3/share/:/opt/gnome/share/

ACLOCAL_FLAGS=-I /opt/gnome/share/aclocal

SSH_CONNECTION=11.12.100.1 52879 11.12.100.4 22

SEQ_LOOKUP_FILE=/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/Data/Tran.dat

PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/local/share/pkgconfig:/usr/lib64/pkgconfig:/usr/share/pkgconfig:/opt/kde3/lib64/pkgconfig:/opt/gnome/lib64/pkgconfig:/opt/gnome/lib64/pkgconfig:/opt/gnome/share/pkgconfig

LESSOPEN=lessopen.sh %s

INFOPATH=/usr/local/info:/usr/share/info:/usr/info:/opt/gnome/share/info

RDP_JAR_PATH=/home/users/quanzx/qiime-software/rdp_classifier_2.2/rdp_classifier-2.2.jar

INCLUDE=/opt/software/compiler/intel/11.1/072/mkl/include

LESSCLOSE=lessclose.sh %s %s

G_BROKEN_FILENAMES=1

COLORTERM=1

_=/usr/bin/env

在 2013年6月14日星期五UTC+8下午2时28分26秒，Will Van Treuren写道：

[yings...@126.com]

this is the error in my installation

quanzx@compile:~/qiime-software/AmpliconNoiseV1.27> make

(cd FCluster && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/FCluster'

make[1]: `FCluster' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/FCluster'

(cd FastaUnique && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/FastaUnique'

make[1]: `FastaUnique' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/FastaUnique'

(cd NDist && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/NDist'

make[1]: `NDist' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/NDist'

(cd PyroDist && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/PyroDist'

make[1]: `PyroDist' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/PyroDist'

(cd PyroNoise && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/PyroNoise'

make[1]: `PyroNoise' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/PyroNoise'

(cd SeqDist && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/SeqDist'

make[1]: `SeqDist' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/SeqDist'

(cd PyroNoiseM && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/PyroNoiseM'

make[1]: `PyroNoiseM' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/PyroNoiseM'

(cd SeqNoise && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/SeqNoise'

make[1]: `SeqNoise' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/SeqNoise'

(cd SplitClusterEven && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/SplitClusterEven'

make[1]: `SplitClusterEven' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/SplitClusterEven'

(cd SplitClusterClust && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/SplitClusterClust'

make[1]: `SplitClusterClust' is up to date.

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/SplitClusterClust'

(cd Perseus && make)

make[1]: Entering directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/Perseus'

cc -O3  -c Perseus.c

Perseus.c:14:24: error: gsl/gsl_sf.h: No such file or directory

Perseus.c:15:29: error: gsl/gsl_randist.h: No such file or directory

make[1]: *** [Perseus.o] Error 1

make[1]: Leaving directory `/home/users/quanzx/qiime-software/AmpliconNoiseV1.27/Perseus'

make: *** [all] Error 2

quanzx@compile:~/qiime-software/AmpliconNoiseV1.27> make install                cp FCluster/FCluster bin

cp FastaUnique/FastaUnique bin

cp NDist/NDist bin

cp PyroDist/PyroDist bin

cp PyroNoise/PyroNoise bin

cp PyroNoiseM/PyroNoiseM bin

cp SeqDist/SeqDist bin

cp SeqNoise/SeqNoise bin

cp SplitClusterEven/SplitClusterEven bin

cp SplitClusterClust/SplitClusterClust bin

cp Perseus/Perseus bin

cp: cannot stat `Perseus/Perseus': No such file or directory

make: *** [install] Error 1

quanzx@compile:~/qiime-software/AmpliconNoiseV1.27>

在 2013年6月14日星期五UTC+8下午2时28分26秒，Will Van Treuren写道：

[Will Van Treuren]

Hi Yingshi, 

Can you try installing a different gsl, specifically the one found at:

http://open-source-box.org/gsl/gsl-1.9.tar.gz

If there are errors can you post the output? If there are no errors can you post the output of the command:

Perseus 

Thanks,

Will 

[yings...@126.com]

I have tried and no error during the installation of gsl.

and i type the command Perseus

 quanzx@compile:~/qiime-software/gsl-1.9> Perseus

-bash: Perseus: command not found

i think maybe the problem of the location to set.

what i have done is 

./configure --prefix=$HOME/qiime-software/gsl-1.9

make

make install

echo "export PATH=$HOME/qiime-software/ gsl-1.9/bin/:$PATH" >> $HOME/.bashrc

source $HOME/.bashrc

what else would you like me to set?
在 2013年6月15日星期六UTC+8上午12时24分27秒，Will Van Treuren写道：

[Will Van Treuren]

Hi,

The path you added seems to have a space in it which I doubt the folder structure actually has (between the bolded characters below)

echo "export PATH=$HOME/qiime-software/ gsl-1.9/bin/:$PATH" >> $HOME/.bashrc

Can you remove the space and try using the commands below?

echo "export PATH=$HOME/qiime-software/gsl-1.9/bin/:$PATH" >> $HOME/.bashrc

source ~/.bashrc

Perseus

And post the output?

Thanks,

Will 

[yings...@126.com]

I'm sorry i type the space in the post. but in my .bashrc don't have the space. so the problem still here

the output of command Perseus is

quanzx@compile:~/qiime-software/gsl-1.9> Perseus

-bash: Perseus: command not found

在 2013年6月16日星期日UTC+8上午12时42分51秒，Will Van Treuren写道：

[Will Van Treuren]

Can you send your .bashrc file to me?

Thanks,

Will 

[yings...@126.com]

the .bashrc file is in attachment

thanks for help me check it 

在 2013年6月16日星期日UTC+8上午2时10分03秒，Will Van Treuren写道：

[Will Van Treuren]

Hi Yingshi,

Your .bashrc file is exceedingly complex. All your 'export PATH' statements except the last one will be ignored because you keep overwriting PATH. Can you send me the output of the command:

ls -lag /home/users/quanzx/qiime-software/AmpliconNoiseV1.27/bin

Thanks,

Will 

[yings...@126.com]

do you think i overwrite PATH is because  everytime i type echo "export PATH=$HOME/bin/:$PATH" >> $HOME/.bashrc followed type  source $HOME/.bashrc?

the output of ls -lag $HOME/qiime-software/AmpliconNoiseV1.27/bin

total 1116

drwxr-xr-x  2 quanzx   4096 2013-06-16 00:09 .

drwxr-xr-x 21 quanzx   4096 2013-06-16 00:10 ..

-rwxr-xr-x  1 quanzx  16958 2013-06-16 00:09 FastaUnique

-rwxr-xr-x  1 quanzx  26034 2013-06-16 00:09 FCluster

-rwxr-xr-x  1 quanzx  78141 2013-06-16 00:09 NDist

-rwxr-xr-x  1 quanzx 171020 2013-06-16 00:09 PyroDist

-rwxr-xr-x  1 quanzx 251506 2013-06-16 00:09 PyroNoise

-rwxr-xr-x  1 quanzx 252582 2013-06-16 00:09 PyroNoiseM

-rwxr-xr-x  1 quanzx  82594 2013-06-16 00:09 SeqDist

-rwxr-xr-x  1 quanzx 188225 2013-06-16 00:09 SeqNoise

-rwxr-xr-x  1 quanzx  16603 2013-06-16 00:09 SplitClusterClust

-rwxr-xr-x  1 quanzx  28354 2013-06-16 00:09 SplitClusterEven

在 2013年6月17日星期一UTC+8下午9时46分21秒，Will Van Treuren写道：

[Will Van Treuren]

Yes, that is the explanation I believe. The output of that last command shows that Perseus is not there, meaning the install has failed. I would assume that the GSL have failed to install correctly, though I am unsure how you should test it. I would recommend removing the current installation of GSL, and trying again. 

Another forum master indicated that you might want to make sure that your GSL has the proper links to headers/preprocessors in the installation. Look at section 2.2 of this to get an idea. 

Best, 

Will 

[yings...@126.com]

i got it. thanks very much 

it's because of the environment variable to set

i add the four environment variable to the .bashrc. Now it worked,but i'm not clear that which variable is the key...

export LD_LIBRARY_PATH=/home/users/quanzx/qiime-software/gsl-1.9/lib/:$LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/home/users/quanzx/qiime-software/gsl-1.9/gsl/:$LD_LIBRARY_PATH

export LIBRARY_PATH=/home/users/quanzx/qiime-software/gsl-1.9/lib/:$LIBRARY_PATH

export C_INCLUDE_PATH=/home/users/quanzx/qiime-software/gsl-1.9/include/:$C_INCLUDE_PATH

在 2013年6月18日星期二UTC+8下午12时56分46秒，Will Van Treuren写道：

[Will Van Treuren]

Hi Yingshi, 

I am not sure which of those paths is essential, but as long as they are not causing problems it seems reasonable to leave them all in there as they will likely not interact with anything else (like having really extensive PATH and PYTHONPATH variables will). 

Thanks for the info as well, we will use it to help future users much more easily. 

Best, 

Will